diff --git a/packages/core/src/config/storage.ts b/packages/core/src/config/storage.ts
index 5de57ab0c..f0b80d88c 100644
--- a/packages/core/src/config/storage.ts
+++ b/packages/core/src/config/storage.ts
@@ -12,6 +12,7 @@ import { getProjectHash, sanitizeCwd } from '../utils/paths.js';
 export const QWEN_DIR = '.qwen';
 export const GOOGLE_ACCOUNTS_FILENAME = 'google_accounts.json';
 export const OAUTH_FILE = 'oauth_creds.json';
+export const SKILL_PROVIDER_CONFIG_DIRS = ['.qwen', '.agent'];
 const TMP_DIR_NAME = 'tmp';
 const BIN_DIR_NAME = 'bin';
 const PROJECT_DIR_NAME = 'projects';
@@ -138,8 +139,11 @@ export class Storage {
     return path.join(this.getExtensionsDir(), 'qwen-extension.json');
   }
 
-  getUserSkillsDir(): string {
-    return path.join(Storage.getGlobalQwenDir(), 'skills');
+  getUserSkillsDirs(): string[] {
+    const homeDir = os.homedir() || os.tmpdir();
+    return SKILL_PROVIDER_CONFIG_DIRS.map((dir) =>
+      path.join(homeDir, dir, 'skills'),
+    );
   }
 
   getHistoryFilePath(): string {
diff --git a/packages/core/src/services/shellExecutionService.ts b/packages/core/src/services/shellExecutionService.ts
index 73fe770ac..e943275bd 100644
--- a/packages/core/src/services/shellExecutionService.ts
+++ b/packages/core/src/services/shellExecutionService.ts
@@ -57,14 +57,10 @@ function getWindowsPathFingerprint(
   env: NodeJS.ProcessEnv,
   pathKeys: string[],
 ): string {
-  return pathKeys
-    .map((key) => `${key}=${env[key] ?? ''}`)
-    .join('\0');
+  return pathKeys.map((key) => `${key}=${env[key] ?? ''}`).join('\0');
 }
 
-function normalizePathEnvForWindows(
-  env: NodeJS.ProcessEnv,
-): NodeJS.ProcessEnv {
+function normalizePathEnvForWindows(env: NodeJS.ProcessEnv): NodeJS.ProcessEnv {
   if (os.platform() !== 'win32') {
     return env;
   }
diff --git a/packages/core/src/skills/skill-manager.test.ts b/packages/core/src/skills/skill-manager.test.ts
index 272d3001d..639234577 100644
--- a/packages/core/src/skills/skill-manager.test.ts
+++ b/packages/core/src/skills/skill-manager.test.ts
@@ -73,6 +73,14 @@ describe('SkillManager', () => {
       if (yamlString.includes('name: regular-skill')) {
         return { name: 'regular-skill', description: 'A regular skill' };
       }
+      if (yamlString.includes('name: shared-skill')) {
+        const desc = yamlString.includes('From qwen dir')
+          ? 'From qwen dir'
+          : yamlString.includes('From agent dir')
+            ? 'From agent dir'
+            : 'A shared skill';
+        return { name: 'shared-skill', description: desc };
+      }
       if (!yamlString.includes('name:')) {
         return { description: 'A test skill' }; // Missing name case
       }
@@ -391,42 +399,61 @@ You are a helpful assistant.
 
   describe('listSkills', () => {
     beforeEach(() => {
-      // Mock directory listing for skills directories (with Dirent objects)
-      vi.mocked(fs.readdir)
-        .mockResolvedValueOnce([
-          {
-            name: 'skill1',
-            isDirectory: () => true,
-            isFile: () => false,
-            isSymbolicLink: () => false,
-          },
-          {
-            name: 'skill2',
-            isDirectory: () => true,
-            isFile: () => false,
-            isSymbolicLink: () => false,
-          },
-          {
-            name: 'not-a-dir.txt',
-            isDirectory: () => false,
-            isFile: () => true,
-            isSymbolicLink: () => false,
-          },
-        ] as unknown as Awaited<ReturnType<typeof fs.readdir>>)
-        .mockResolvedValueOnce([
-          {
-            name: 'skill3',
-            isDirectory: () => true,
-            isFile: () => false,
-            isSymbolicLink: () => false,
-          },
-          {
-            name: 'skill1',
-            isDirectory: () => true,
-            isFile: () => false,
-            isSymbolicLink: () => false,
-          },
-        ] as unknown as Awaited<ReturnType<typeof fs.readdir>>);
+      // Mock directory listing based on path to handle multiple base dirs per level.
+      // Use path.join to construct expected paths so separators match on all platforms.
+      const projectQwenSkillsDir = path.join(
+        '/test/project',
+        '.qwen',
+        'skills',
+      );
+      const userQwenSkillsDir = path.join('/home/user', '.qwen', 'skills');
+
+      // eslint-disable-next-line @typescript-eslint/no-explicit-any
+      vi.mocked(fs.readdir).mockImplementation((dirPath: any) => {
+        const pathStr = String(dirPath);
+        if (pathStr === projectQwenSkillsDir) {
+          return Promise.resolve([
+            {
+              name: 'skill1',
+              isDirectory: () => true,
+              isFile: () => false,
+              isSymbolicLink: () => false,
+            },
+            {
+              name: 'skill2',
+              isDirectory: () => true,
+              isFile: () => false,
+              isSymbolicLink: () => false,
+            },
+            {
+              name: 'not-a-dir.txt',
+              isDirectory: () => false,
+              isFile: () => true,
+              isSymbolicLink: () => false,
+            },
+          ] as unknown as Awaited<ReturnType<typeof fs.readdir>>);
+        }
+        if (pathStr === userQwenSkillsDir) {
+          return Promise.resolve([
+            {
+              name: 'skill3',
+              isDirectory: () => true,
+              isFile: () => false,
+              isSymbolicLink: () => false,
+            },
+            {
+              name: 'skill1',
+              isDirectory: () => true,
+              isFile: () => false,
+              isSymbolicLink: () => false,
+            },
+          ] as unknown as Awaited<ReturnType<typeof fs.readdir>>);
+        }
+        // Other provider dirs (.agent, .cursor, .codex, .claude) return empty
+        return Promise.resolve(
+          [] as unknown as Awaited<ReturnType<typeof fs.readdir>>,
+        );
+      });
 
       vi.mocked(fs.access).mockResolvedValue(undefined);
 
@@ -483,6 +510,66 @@ Skill 3 content`);
       expect(projectSkills.every((s) => s.level === 'project')).toBe(true);
     });
 
+    it('should deduplicate same-name skills across provider dirs within a level', async () => {
+      // Override readdir to return the same skill name from both .qwen and .agent dirs
+      vi.mocked(fs.readdir).mockReset();
+      const projectQwenDir = path.join('/test/project', '.qwen', 'skills');
+      const projectAgentDir = path.join('/test/project', '.agent', 'skills');
+
+      // eslint-disable-next-line @typescript-eslint/no-explicit-any
+      vi.mocked(fs.readdir).mockImplementation((dirPath: any) => {
+        const pathStr = String(dirPath);
+        if (pathStr === projectQwenDir) {
+          return Promise.resolve([
+            {
+              name: 'shared-skill',
+              isDirectory: () => true,
+              isFile: () => false,
+              isSymbolicLink: () => false,
+            },
+          ] as unknown as Awaited<ReturnType<typeof fs.readdir>>);
+        }
+        if (pathStr === projectAgentDir) {
+          return Promise.resolve([
+            {
+              name: 'shared-skill',
+              isDirectory: () => true,
+              isFile: () => false,
+              isSymbolicLink: () => false,
+            },
+          ] as unknown as Awaited<ReturnType<typeof fs.readdir>>);
+        }
+        return Promise.resolve(
+          [] as unknown as Awaited<ReturnType<typeof fs.readdir>>,
+        );
+      });
+
+      vi.mocked(fs.readFile).mockImplementation((filePath) => {
+        const pathStr = String(filePath);
+        if (pathStr.includes('.qwen') && pathStr.includes('shared-skill')) {
+          return Promise.resolve(
+            `---\nname: shared-skill\ndescription: From qwen dir\n---\nQwen content`,
+          );
+        }
+        if (pathStr.includes('.agent') && pathStr.includes('shared-skill')) {
+          return Promise.resolve(
+            `---\nname: shared-skill\ndescription: From agent dir\n---\nAgent content`,
+          );
+        }
+        return Promise.reject(new Error('File not found'));
+      });
+
+      const skills = await manager.listSkills({
+        level: 'project',
+        force: true,
+      });
+
+      // Only one instance should remain, from .qwen (first in PROVIDER_CONFIG_DIRS)
+      expect(skills).toHaveLength(1);
+      expect(skills[0].name).toBe('shared-skill');
+      expect(skills[0].description).toBe('From qwen dir');
+    });
+
     it('should handle empty directories', async () => {
       vi.mocked(fs.readdir).mockReset();
       vi.mocked(fs.readdir).mockResolvedValue(
@@ -504,27 +591,33 @@ Skill 3 content`);
     });
   });
 
-  describe('getSkillsBaseDir', () => {
-    it('should return project-level base dir', () => {
-      const baseDir = manager.getSkillsBaseDir('project');
+  describe('getSkillsBaseDirs', () => {
+    it('should return all project-level base dirs', () => {
+      const baseDirs = manager.getSkillsBaseDirs('project');
 
-      expect(baseDir).toBe(path.join('/test/project', '.qwen', 'skills'));
+      expect(baseDirs).toHaveLength(2);
+      expect(baseDirs).toContain(path.join('/test/project', '.qwen', 'skills'));
+      expect(baseDirs).toContain(
+        path.join('/test/project', '.agent', 'skills'),
+      );
     });
 
-    it('should return user-level base dir', () => {
-      const baseDir = manager.getSkillsBaseDir('user');
+    it('should return all user-level base dirs', () => {
+      const baseDirs = manager.getSkillsBaseDirs('user');
 
-      expect(baseDir).toBe(path.join('/home/user', '.qwen', 'skills'));
+      expect(baseDirs).toHaveLength(2);
+      expect(baseDirs).toContain(path.join('/home/user', '.qwen', 'skills'));
+      expect(baseDirs).toContain(path.join('/home/user', '.agent', 'skills'));
     });
 
     it('should return bundled-level base dir', () => {
-      const baseDir = manager.getSkillsBaseDir('bundled');
+      const baseDirs = manager.getSkillsBaseDirs('bundled');
 
-      expect(baseDir).toMatch(/skills[/\\]bundled$/);
+      expect(baseDirs[0]).toMatch(/skills[/\\]bundled$/);
     });
 
     it('should throw for extension level', () => {
-      expect(() => manager.getSkillsBaseDir('extension')).toThrow(
+      expect(() => manager.getSkillsBaseDirs('extension')).toThrow(
         'Extension skills do not have a base directory',
       );
     });
diff --git a/packages/core/src/skills/skill-manager.ts b/packages/core/src/skills/skill-manager.ts
index b6636a627..fbeb18b8d 100644
--- a/packages/core/src/skills/skill-manager.ts
+++ b/packages/core/src/skills/skill-manager.ts
@@ -22,6 +22,7 @@ import type { Config } from '../config/config.js';
 import { validateConfig } from './skill-load.js';
 import { createDebugLogger } from '../utils/debugLogger.js';
 import { normalizeContent } from '../utils/textUtils.js';
+import { SKILL_PROVIDER_CONFIG_DIRS } from '../config/storage.js';
 
 const debugLogger = createDebugLogger('SKILL_MANAGER');
 
@@ -428,20 +429,20 @@ export class SkillManager {
    * Gets the base directory for skills at a specific level.
    *
    * @param level - Storage level
-   * @returns Absolute directory path
+   * @returns Absolute directory paths
    */
-  getSkillsBaseDir(level: SkillLevel): string {
+  getSkillsBaseDirs(level: SkillLevel): string[] {
     switch (level) {
       case 'project':
-        return path.join(
-          this.config.getProjectRoot(),
-          QWEN_CONFIG_DIR,
-          SKILLS_CONFIG_DIR,
+        return SKILL_PROVIDER_CONFIG_DIRS.map((v) =>
+          path.join(this.config.getProjectRoot(), v, SKILLS_CONFIG_DIR),
         );
       case 'user':
-        return path.join(os.homedir(), QWEN_CONFIG_DIR, SKILLS_CONFIG_DIR);
+        return SKILL_PROVIDER_CONFIG_DIRS.map((v) =>
+          path.join(os.homedir(), v, SKILLS_CONFIG_DIR),
+        );
       case 'bundled':
-        return this.bundledSkillsDir;
+        return [this.bundledSkillsDir];
       case 'extension':
         throw new Error(
           'Extension skills do not have a base directory; they are loaded from active extensions.',
@@ -499,9 +500,26 @@ export class SkillManager {
       return skills;
     }
 
-    const baseDir = this.getSkillsBaseDir(level);
-    debugLogger.debug(`Loading ${level} level skills from: ${baseDir}`);
-    const skills = await this.loadSkillsFromDir(baseDir, level);
+    // Iterate provider directories in PROVIDER_CONFIG_DIRS order.
+    // The first directory that contains a skill with a given name wins,
+    // so the order defines implicit precedence (.qwen > .agent > .cursor > ...).
+    const baseDirs = this.getSkillsBaseDirs(level);
+    const skills: SkillConfig[] = [];
+    const seenNames = new Set<string>();
+    for (const baseDir of baseDirs) {
+      debugLogger.debug(`Loading ${level} level skills from: ${baseDir}`);
+      const skillsFromDir = await this.loadSkillsFromDir(baseDir, level);
+      for (const skill of skillsFromDir) {
+        if (seenNames.has(skill.name)) {
+          debugLogger.debug(
+            `Skipping duplicate skill at ${level} level: ${skill.name} from ${baseDir}`,
+          );
+          continue;
+        }
+        seenNames.add(skill.name);
+        skills.push(skill);
+      }
+    }
     debugLogger.debug(`Loaded ${skills.length} ${level} level skills`);
     return skills;
   }
@@ -624,7 +642,8 @@ export class SkillManager {
   private updateWatchersFromCache(): void {
     const watchTargets = new Set<string>(
       (['project', 'user'] as const)
-        .map((level) => this.getSkillsBaseDir(level))
+        .map((level) => this.getSkillsBaseDirs(level))
+        .reduce((acc, baseDirs) => acc.concat(baseDirs), [])
         .filter((baseDir) => fsSync.existsSync(baseDir)),
     );
 
@@ -680,7 +699,7 @@ export class SkillManager {
   }
 
   private async ensureUserSkillsDir(): Promise<void> {
-    const baseDir = this.getSkillsBaseDir('user');
+    const baseDir = path.join(os.homedir(), QWEN_CONFIG_DIR, SKILLS_CONFIG_DIR);
     try {
       await fs.mkdir(baseDir, { recursive: true });
     } catch (error) {
diff --git a/packages/core/src/tools/ls.test.ts b/packages/core/src/tools/ls.test.ts
index da6273eb1..204289e61 100644
--- a/packages/core/src/tools/ls.test.ts
+++ b/packages/core/src/tools/ls.test.ts
@@ -43,7 +43,7 @@ describe('LSTool', () => {
       }),
       getTruncateToolOutputLines: () => 1000,
       storage: {
-        getUserSkillsDir: () => userSkillsBase,
+        getUserSkillsDirs: () => [userSkillsBase],
       },
     } as unknown as Config;
 
diff --git a/packages/core/src/tools/ls.ts b/packages/core/src/tools/ls.ts
index 877a1274b..a4283417b 100644
--- a/packages/core/src/tools/ls.ts
+++ b/packages/core/src/tools/ls.ts
@@ -9,7 +9,7 @@ import path from 'node:path';
 import type { ToolInvocation, ToolResult } from './tools.js';
 import { BaseDeclarativeTool, BaseToolInvocation, Kind } from './tools.js';
 import { makeRelative, shortenPath } from '../utils/paths.js';
-import { isSubpath } from '../utils/paths.js';
+import { isSubpaths } from '../utils/paths.js';
 import type { Config } from '../config/config.js';
 import { DEFAULT_FILE_FILTERING_OPTIONS } from '../config/constants.js';
 import { ToolErrorType } from './tool-error.js';
@@ -335,8 +335,8 @@ export class LSTool extends BaseDeclarativeTool<LSToolParams, ToolResult> {
       return `Path must be absolute: ${params.path}`;
     }
 
-    const userSkillsBase = this.config.storage.getUserSkillsDir();
-    const isUnderUserSkills = isSubpath(userSkillsBase, params.path);
+    const userSkillsBases = this.config.storage.getUserSkillsDirs();
+    const isUnderUserSkills = isSubpaths(userSkillsBases, params.path);
 
     const workspaceContext = this.config.getWorkspaceContext();
     if (
diff --git a/packages/core/src/tools/read-file.test.ts b/packages/core/src/tools/read-file.test.ts
index 1878c3805..ebc9cb27b 100644
--- a/packages/core/src/tools/read-file.test.ts
+++ b/packages/core/src/tools/read-file.test.ts
@@ -40,7 +40,7 @@ describe('ReadFileTool', () => {
       getWorkspaceContext: () => createMockWorkspaceContext(tempRootDir),
       storage: {
         getProjectTempDir: () => path.join(tempRootDir, '.temp'),
-        getUserSkillsDir: () => path.join(os.homedir(), '.qwen', 'skills'),
+        getUserSkillsDirs: () => [path.join(os.homedir(), '.qwen', 'skills')],
       },
       getTruncateToolOutputThreshold: () => 2500,
       getTruncateToolOutputLines: () => 500,
diff --git a/packages/core/src/tools/read-file.ts b/packages/core/src/tools/read-file.ts
index 2e0a1c228..4a9c3bd9a 100644
--- a/packages/core/src/tools/read-file.ts
+++ b/packages/core/src/tools/read-file.ts
@@ -21,7 +21,7 @@ import { FileOperation } from '../telemetry/metrics.js';
 import { getProgrammingLanguage } from '../telemetry/telemetry-utils.js';
 import { logFileOperation } from '../telemetry/loggers.js';
 import { FileOperationEvent } from '../telemetry/types.js';
-import { isSubpath } from '../utils/paths.js';
+import { isSubpaths, isSubpath } from '../utils/paths.js';
 import { Storage } from '../config/storage.js';
 
 /**
@@ -187,7 +187,7 @@ export class ReadFileTool extends BaseDeclarativeTool<
     const workspaceContext = this.config.getWorkspaceContext();
     const globalTempDir = Storage.getGlobalTempDir();
     const projectTempDir = this.config.storage.getProjectTempDir();
-    const userSkillsDir = this.config.storage.getUserSkillsDir();
+    const userSkillsDirs = this.config.storage.getUserSkillsDirs();
     const arenaDir = Storage.getGlobalArenaDir();
     const resolvedFilePath = path.resolve(filePath);
     const osTempDir = os.tmpdir();
@@ -195,8 +195,9 @@ export class ReadFileTool extends BaseDeclarativeTool<
       isSubpath(projectTempDir, resolvedFilePath) ||
       isSubpath(globalTempDir, resolvedFilePath) ||
       isSubpath(osTempDir, resolvedFilePath);
+
+    const isWithinUserSkills = isSubpaths(userSkillsDirs, resolvedFilePath);
     const isWithinArenaDir = isSubpath(arenaDir, resolvedFilePath);
-    const isWithinUserSkills = isSubpath(userSkillsDir, resolvedFilePath);
 
     if (
       !workspaceContext.isPathWithinWorkspace(filePath) &&
diff --git a/packages/core/src/tools/shell.test.ts b/packages/core/src/tools/shell.test.ts
index e9aa4f850..95222af5d 100644
--- a/packages/core/src/tools/shell.test.ts
+++ b/packages/core/src/tools/shell.test.ts
@@ -57,7 +57,7 @@ describe('ShellTool', () => {
         .fn()
         .mockReturnValue(createMockWorkspaceContext('/test/dir')),
       storage: {
-        getUserSkillsDir: vi.fn().mockReturnValue('/test/dir/.qwen/skills'),
+        getUserSkillsDirs: vi.fn().mockReturnValue(['/test/dir/.qwen/skills']),
         getProjectTempDir: vi.fn().mockReturnValue('/tmp/qwen-temp'),
       },
       getTruncateToolOutputThreshold: vi.fn().mockReturnValue(0),
diff --git a/packages/core/src/tools/shell.ts b/packages/core/src/tools/shell.ts
index 54ecf30f8..67cd4cc38 100644
--- a/packages/core/src/tools/shell.ts
+++ b/packages/core/src/tools/shell.ts
@@ -34,7 +34,7 @@ import type {
 import { ShellExecutionService } from '../services/shellExecutionService.js';
 import { formatMemoryUsage } from '../utils/formatters.js';
 import type { AnsiOutput } from '../utils/terminalSerializer.js';
-import { isSubpath } from '../utils/paths.js';
+import { isSubpaths } from '../utils/paths.js';
 import {
   getCommandRoots,
   isCommandAllowed,
@@ -622,10 +622,10 @@ export class ShellTool extends BaseDeclarativeTool<
         return 'Directory must be an absolute path.';
       }
 
-      const userSkillsDir = this.config.storage.getUserSkillsDir();
+      const userSkillsDirs = this.config.storage.getUserSkillsDirs();
       const resolvedDirectoryPath = path.resolve(params.directory);
-      const isWithinUserSkills = isSubpath(
-        userSkillsDir,
+      const isWithinUserSkills = isSubpaths(
+        userSkillsDirs,
         resolvedDirectoryPath,
       );
       if (isWithinUserSkills) {
diff --git a/packages/core/src/utils/paths.ts b/packages/core/src/utils/paths.ts
index dc4434ece..6e6bdfa49 100644
--- a/packages/core/src/utils/paths.ts
+++ b/packages/core/src/utils/paths.ts
@@ -241,6 +241,10 @@ export function isSubpath(parentPath: string, childPath: string): boolean {
   );
 }
 
+export function isSubpaths(parentPath: string[], childPath: string): boolean {
+  return parentPath.some((p) => isSubpath(p, childPath));
+}
+
 /**
  * Resolves a path with tilde (~) expansion and relative path resolution.
  * Handles tilde expansion for home directory and resolves relative paths