diff --git a/packages/cli/src/ui/commands/languageCommand.test.ts b/packages/cli/src/ui/commands/languageCommand.test.ts
index e8ebaac01..e7e7bf28e 100644
--- a/packages/cli/src/ui/commands/languageCommand.test.ts
+++ b/packages/cli/src/ui/commands/languageCommand.test.ts
@@ -750,7 +750,7 @@ describe('languageCommand', () => {
       expect(fs.writeFileSync).not.toHaveBeenCalled();
     });
 
-    it('should overwrite existing file when output language setting differs', () => {
+    it('should NOT overwrite existing file even when output language setting differs', () => {
       vi.mocked(fs.existsSync).mockReturnValue(true);
       vi.mocked(fs.readFileSync).mockReturnValue(
         `# Output language preference: English
@@ -760,11 +760,8 @@ describe('languageCommand', () => {
 
       initializeLlmOutputLanguage('Japanese');
 
-      expect(fs.writeFileSync).toHaveBeenCalledWith(
-        expect.stringContaining('output-language.md'),
-        expect.stringContaining('Japanese'),
-        'utf-8',
-      );
+      // Should NOT overwrite - user's existing file takes precedence
+      expect(fs.writeFileSync).not.toHaveBeenCalled();
     });
 
     it('should resolve auto setting to detected system language', () => {
diff --git a/packages/cli/src/utils/languageUtils.test.ts b/packages/cli/src/utils/languageUtils.test.ts
index 39582af75..63e793015 100644
--- a/packages/cli/src/utils/languageUtils.test.ts
+++ b/packages/cli/src/utils/languageUtils.test.ts
@@ -309,12 +309,12 @@ describe('languageUtils', () => {
       );
     });
 
-    it('should NOT overwrite file when content matches resolved language', () => {
+    it('should NOT overwrite file when it already exists with valid content', () => {
       vi.mocked(fs.existsSync).mockReturnValue(true);
       vi.mocked(i18n.detectSystemLanguage).mockReturnValue('en');
       vi.mocked(fs.readFileSync).mockReturnValue(
-        `# Output language preference: English
-<!-- qwen-code:llm-output-language: English -->
+        `# Output language preference: French
+<!-- qwen-code:llm-output-language: French -->
 `,
       );
 
@@ -323,21 +323,18 @@ describe('languageUtils', () => {
       expect(fs.writeFileSync).not.toHaveBeenCalled();
     });
 
-    it('should overwrite file when language setting differs', () => {
+    it('should NOT overwrite file even when setting differs from existing content', () => {
       vi.mocked(fs.existsSync).mockReturnValue(true);
       vi.mocked(fs.readFileSync).mockReturnValue(
-        `# Output language preference: English
-<!-- qwen-code:llm-output-language: English -->
+        `# Output language preference: French
+<!-- qwen-code:llm-output-language: French -->
 `,
       );
 
       initializeLlmOutputLanguage('Japanese');
 
-      expect(fs.writeFileSync).toHaveBeenCalledWith(
-        expect.stringContaining('output-language.md'),
-        expect.stringContaining('Japanese'),
-        'utf-8',
-      );
+      // Should NOT overwrite - user's existing file takes precedence
+      expect(fs.writeFileSync).not.toHaveBeenCalled();
     });
 
     it('should resolve "auto" to detected system language', () => {
diff --git a/packages/cli/src/utils/languageUtils.ts b/packages/cli/src/utils/languageUtils.ts
index cb4e06c4d..722a7a1c7 100644
--- a/packages/cli/src/utils/languageUtils.ts
+++ b/packages/cli/src/utils/languageUtils.ts
@@ -175,17 +175,19 @@ export function updateOutputLanguageFile(settingValue: string): void {
  * @param outputLanguage - The output language setting value (e.g., 'auto', 'Chinese', etc.)
  *
  * Behavior:
- * - Resolves the setting value ('auto' -> detected system language, or use as-is)
- * - Ensures the rule file matches the resolved language
- * - Creates the file if it doesn't exist
+ * - If the rule file already exists and contains a valid language setting, do nothing (preserve user modifications)
+ * - If the rule file doesn't exist, create it with the resolved language ('auto' -> detected system language, or use as-is)
  */
 export function initializeLlmOutputLanguage(outputLanguage?: string): void {
-  // Resolve 'auto' or undefined to the detected system language
-  const resolved = resolveOutputLanguage(outputLanguage);
+  // Check if the file already exists and has valid content
   const currentFileLanguage = readOutputLanguageFromFile();
 
-  // Only write if the file doesn't match the resolved language
-  if (currentFileLanguage !== resolved) {
-    writeOutputLanguageFile(resolved);
+  // If file exists with valid language, preserve user's setting - do nothing
+  if (currentFileLanguage) {
+    return;
   }
+
+  // File doesn't exist or has invalid content, create it with resolved language
+  const resolved = resolveOutputLanguage(outputLanguage);
+  writeOutputLanguageFile(resolved);
 }