diff --git a/packages/core/src/services/gitInit.ts b/packages/core/src/services/gitInit.ts
new file mode 100644
index 000000000..4756c0466
--- /dev/null
+++ b/packages/core/src/services/gitInit.ts
@@ -0,0 +1,14 @@
+/**
+ * @license
+ * Copyright 2025 Qwen Team
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import type { SimpleGit } from 'simple-git';
+
+export async function initRepositoryWithMainBranch(
+  git: SimpleGit,
+): Promise<void> {
+  await git.init(false);
+  await git.raw(['symbolic-ref', 'HEAD', 'refs/heads/main']);
+}
diff --git a/packages/core/src/services/gitService.test.ts b/packages/core/src/services/gitService.test.ts
index 7ef871274..10cde1067 100644
--- a/packages/core/src/services/gitService.test.ts
+++ b/packages/core/src/services/gitService.test.ts
@@ -162,12 +162,27 @@ describe('GitService', () => {
       expect(actualConfigContent).toBe(expectedConfigContent);
     });
 
+    it('should use the shadow git config during repository setup', async () => {
+      const service = new GitService(projectRoot, storage);
+      await service.setupShadowGitRepository();
+
+      expect(hoistedMockEnv).toHaveBeenCalledWith({
+        HOME: repoDir,
+        XDG_CONFIG_HOME: repoDir,
+      });
+    });
+
     it('should initialize git repo in historyDir if not already initialized', async () => {
       hoistedMockCheckIsRepo.mockResolvedValue(false);
       const service = new GitService(projectRoot, storage);
       await service.setupShadowGitRepository();
       expect(hoistedMockSimpleGit).toHaveBeenCalledWith(repoDir);
-      expect(hoistedMockInit).toHaveBeenCalled();
+      expect(hoistedMockInit).toHaveBeenCalledWith(false);
+      expect(hoistedMockRaw).toHaveBeenCalledWith([
+        'symbolic-ref',
+        'HEAD',
+        'refs/heads/main',
+      ]);
     });
 
     it('should initialize git repo when root repo check throws', async () => {
@@ -184,6 +199,7 @@ describe('GitService', () => {
       const service = new GitService(projectRoot, storage);
       await service.setupShadowGitRepository();
       expect(hoistedMockInit).not.toHaveBeenCalled();
+      expect(hoistedMockRaw).not.toHaveBeenCalled();
     });
 
     it('should copy .gitignore from projectRoot if it exists', async () => {
diff --git a/packages/core/src/services/gitService.ts b/packages/core/src/services/gitService.ts
index 9a220d35a..da29cf014 100644
--- a/packages/core/src/services/gitService.ts
+++ b/packages/core/src/services/gitService.ts
@@ -11,6 +11,7 @@ import type { SimpleGit } from 'simple-git';
 import { simpleGit, CheckRepoActions } from 'simple-git';
 import type { Storage } from '../config/storage.js';
 import { isNodeError } from '../utils/errors.js';
+import { initRepositoryWithMainBranch } from './gitInit.js';
 
 export class GitService {
   private projectRoot: string;
@@ -57,7 +58,11 @@ export class GitService {
       '[user]\n  name = Qwen Code\n  email = qwen-code@qwen.ai\n[commit]\n  gpgsign = false\n';
     await fs.writeFile(gitConfigPath, gitConfigContent);
 
-    const repo = simpleGit(repoDir);
+    const repo = simpleGit(repoDir).env({
+      // Prevent git from using the user's global git config.
+      HOME: repoDir,
+      XDG_CONFIG_HOME: repoDir,
+    });
     let isRepoDefined = false;
     try {
       isRepoDefined = await repo.checkIsRepo(CheckRepoActions.IS_REPO_ROOT);
@@ -68,10 +73,7 @@ export class GitService {
     }
 
     if (!isRepoDefined) {
-      await repo.init(false, {
-        '--initial-branch': 'main',
-      });
-
+      await initRepositoryWithMainBranch(repo);
       await repo.commit('Initial commit', { '--allow-empty': null });
     }
 
diff --git a/packages/core/src/services/gitWorktreeService.test.ts b/packages/core/src/services/gitWorktreeService.test.ts
index f34eb1ca2..acfafc39e 100644
--- a/packages/core/src/services/gitWorktreeService.test.ts
+++ b/packages/core/src/services/gitWorktreeService.test.ts
@@ -135,6 +135,43 @@ describe('GitWorktreeService', () => {
     expect(hoistedMockCheckIsRepo).toHaveBeenNthCalledWith(2);
   });
 
+  it('initializeRepository should initialize a new repo on main', async () => {
+    hoistedMockCheckIsRepo.mockResolvedValue(false);
+    const service = new GitWorktreeService('/repo');
+
+    const result = await service.initializeRepository();
+
+    expect(result).toEqual({ initialized: true });
+    expect(hoistedMockInit).toHaveBeenCalledWith(false);
+    expect(hoistedMockRaw).toHaveBeenCalledWith([
+      'symbolic-ref',
+      'HEAD',
+      'refs/heads/main',
+    ]);
+    expect(hoistedMockAdd).toHaveBeenCalledWith('.');
+    expect(hoistedMockCommit).toHaveBeenCalledWith('Initial commit', {
+      '--allow-empty': null,
+    });
+    expect(hoistedMockInit.mock.invocationCallOrder[0]!).toBeLessThan(
+      hoistedMockRaw.mock.invocationCallOrder[0]!,
+    );
+    expect(hoistedMockRaw.mock.invocationCallOrder[0]!).toBeLessThan(
+      hoistedMockCommit.mock.invocationCallOrder[0]!,
+    );
+  });
+
+  it('initializeRepository should not update HEAD for an existing repo', async () => {
+    hoistedMockCheckIsRepo.mockResolvedValue(true);
+    const service = new GitWorktreeService('/repo');
+
+    const result = await service.initializeRepository();
+
+    expect(result).toEqual({ initialized: false });
+    expect(hoistedMockInit).not.toHaveBeenCalled();
+    expect(hoistedMockRaw).not.toHaveBeenCalled();
+    expect(hoistedMockCommit).not.toHaveBeenCalled();
+  });
+
   it('createWorktree should create a sanitized branch and worktree path', async () => {
     const service = new GitWorktreeService('/repo');
 
diff --git a/packages/core/src/services/gitWorktreeService.ts b/packages/core/src/services/gitWorktreeService.ts
index 6ceebf11e..bec5ca6ae 100644
--- a/packages/core/src/services/gitWorktreeService.ts
+++ b/packages/core/src/services/gitWorktreeService.ts
@@ -12,6 +12,7 @@ import type { SimpleGit } from 'simple-git';
 import { Storage } from '../config/storage.js';
 import { isCommandAvailable } from '../utils/shell-utils.js';
 import { isNodeError } from '../utils/errors.js';
+import { initRepositoryWithMainBranch } from './gitInit.js';
 
 /**
  * Commit message used for the baseline snapshot in worktrees.
@@ -185,7 +186,7 @@ export class GitWorktreeService {
     }
 
     try {
-      await this.git.init(false, { '--initial-branch': 'main' });
+      await initRepositoryWithMainBranch(this.git);
 
       // Create initial commit so we can create worktrees
       await this.git.add('.');