diff --git a/packages/core/src/permissions/permission-manager.test.ts b/packages/core/src/permissions/permission-manager.test.ts
index 5b1048d5cb..505a80d15b 100644
--- a/packages/core/src/permissions/permission-manager.test.ts
+++ b/packages/core/src/permissions/permission-manager.test.ts
@@ -228,6 +228,24 @@ describe('matchesCommandPattern', () => {
       expect(matchesCommandPattern('npm run *', 'npm run build')).toBe(true);
     });
 
+    it('matches commands with leading env var assignments', async () => {
+      expect(
+        matchesCommandPattern(
+          'python3 *',
+          'PYTHONPATH=/tmp/lib python3 -c "print(1)"',
+        ),
+      ).toBe(true);
+    });
+
+    it('matches commands containing embedded newlines (dotAll)', async () => {
+      expect(
+        matchesCommandPattern(
+          'python3 *',
+          'python3 -c "\nimport sys\nprint(sys.version)\n"',
+        ),
+      ).toBe(true);
+    });
+
     it('space-star requires word boundary (ls * does not match lsof)', async () => {
       expect(matchesCommandPattern('ls *', 'ls -la')).toBe(true);
       expect(matchesCommandPattern('ls *', 'lsof')).toBe(false);
diff --git a/packages/core/src/permissions/rule-parser.ts b/packages/core/src/permissions/rule-parser.ts
index 6ca9e83632..dd3641f785 100644
--- a/packages/core/src/permissions/rule-parser.ts
+++ b/packages/core/src/permissions/rule-parser.ts
@@ -7,6 +7,7 @@
 import path from 'node:path';
 import os from 'node:os';
 import picomatch from 'picomatch';
+import { parse } from 'shell-quote';
 
 /**
  * Normalize a filesystem path to use POSIX-style forward slashes.
@@ -606,6 +607,7 @@ export function matchesCommandPattern(
 ): boolean {
   // This function matches a single pattern against a single simple command.
   // Compound command splitting is handled by the caller (PermissionManager).
+  const normalizedCommand = stripLeadingVariableAssignments(command);
 
   // Special case: lone `*` matches any single command
   if (pattern === '*') {
@@ -616,7 +618,10 @@ export function matchesCommandPattern(
     // No wildcards: prefix matching (backward compat).
     // "git commit" matches "git commit" and "git commit -m test"
     // but NOT "gitcommit".
-    return command === pattern || command.startsWith(pattern + ' ');
+    return (
+      normalizedCommand === pattern ||
+      normalizedCommand.startsWith(pattern + ' ')
+    );
   }
 
   // Build regex from glob pattern with word-boundary semantics.
@@ -665,9 +670,9 @@ export function matchesCommandPattern(
   regex += '$';
 
   try {
-    return new RegExp(regex).test(command);
+    return new RegExp(regex, 's').test(normalizedCommand);
   } catch {
-    return command === pattern;
+    return normalizedCommand === pattern;
   }
 }
 
@@ -678,6 +683,44 @@ function escapeRegex(s: string): string {
   return s.replace(/[.+?^${}()|[\]\\]/g, '\\$&');
 }
 
+const ENV_ASSIGNMENT_REGEX = /^[A-Za-z_][A-Za-z0-9_]*=/;
+
+function stripLeadingVariableAssignments(command: string): string {
+  const trimmed = command.trim();
+  if (!trimmed) {
+    return trimmed;
+  }
+
+  try {
+    const tokens: string[] = [];
+
+    for (const token of parse(trimmed)) {
+      if (typeof token === 'string') {
+        tokens.push(token);
+      } else if (
+        token &&
+        typeof token === 'object' &&
+        'op' in token &&
+        typeof token.op === 'string'
+      ) {
+        tokens.push(token.op);
+      }
+    }
+
+    let firstCommandToken = 0;
+    while (
+      firstCommandToken < tokens.length &&
+      ENV_ASSIGNMENT_REGEX.test(tokens[firstCommandToken]!)
+    ) {
+      firstCommandToken++;
+    }
+
+    return tokens.slice(firstCommandToken).join(' ');
+  } catch {
+    return trimmed;
+  }
+}
+
 // ─────────────────────────────────────────────────────────────────────────────
 // File path matching (gitignore-style)
 // ─────────────────────────────────────────────────────────────────────────────
diff --git a/packages/core/src/utils/shell-utils.test.ts b/packages/core/src/utils/shell-utils.test.ts
index 0cdeaee88e..b95e95c7b1 100644
--- a/packages/core/src/utils/shell-utils.test.ts
+++ b/packages/core/src/utils/shell-utils.test.ts
@@ -29,11 +29,15 @@ vi.mock('os', () => ({
 }));
 
 const mockQuote = vi.hoisted(() => vi.fn());
-const mockParse = vi.hoisted(() => vi.fn());
-vi.mock('shell-quote', () => ({
-  quote: mockQuote,
-  parse: mockParse,
-}));
+vi.mock('shell-quote', async () => {
+  const actual =
+    await vi.importActual<typeof import('shell-quote')>('shell-quote');
+
+  return {
+    ...actual,
+    quote: mockQuote,
+  };
+});
 
 let config: Config;
 
@@ -42,7 +46,6 @@ beforeEach(() => {
   mockQuote.mockImplementation((args: string[]) =>
     args.map((arg) => `'${arg}'`).join(' '),
   );
-  mockParse.mockImplementation((cmd: string) => cmd.split(' '));
   config = {
     getCoreTools: () => [],
     getPermissionsDeny: () => [],
@@ -453,6 +456,20 @@ describe('getCommandRoots', () => {
     const result = getCommandRoots('echo hello >| out.txt');
     expect(result).toEqual(['echo']);
   });
+
+  it('should skip leading env var assignments', async () => {
+    expect(
+      getCommandRoots(
+        'PYTHONPATH=/Users/jinjing/.qwen/skills/scripts python3 -c "print(1)"',
+      ),
+    ).toEqual(['python3']);
+  });
+
+  it('should preserve quoted Windows paths with spaces', async () => {
+    expect(getCommandRoots('"C:\\Program Files\\foo\\bar.exe" arg1')).toEqual([
+      'bar.exe',
+    ]);
+  });
 });
 
 describe('stripShellWrapper', () => {
diff --git a/packages/core/src/utils/shell-utils.ts b/packages/core/src/utils/shell-utils.ts
index 8eeb19eaad..ac4a2d0d51 100644
--- a/packages/core/src/utils/shell-utils.ts
+++ b/packages/core/src/utils/shell-utils.ts
@@ -8,7 +8,7 @@ import type { AnyToolInvocation } from '../index.js';
 import type { Config } from '../config/config.js';
 import os from 'node:os';
 import path from 'node:path';
-import { quote } from 'shell-quote';
+import { parse, quote } from 'shell-quote';
 import { doesToolInvocationMatch } from './tool-utils.js';
 import { isShellCommandReadOnly } from './shellReadOnlyChecker.js';
 import {
@@ -40,6 +40,7 @@ export interface ShellConfiguration {
 }
 
 let cachedBashPath: string | undefined;
+const ENV_ASSIGNMENT_REGEX = /^[A-Za-z_][A-Za-z0-9_]*=/;
 
 /**
  * Attempts to find the Git Bash executable path on Windows.
@@ -289,11 +290,8 @@ export function splitCommands(command: string): string[] {
 
 /**
  * Extracts the root command from a given shell command string.
- * This is used to identify the base command for permission checks.
- * @param command The shell command string to parse
- * @returns The root command name, or undefined if it cannot be determined
- * @example getCommandRoot("ls -la /tmp") returns "ls"
- * @example getCommandRoot("git status && npm test") returns "git"
+ * Skips leading env var assignments (VAR=value) so that
+ * `PYTHONPATH=/tmp python3 -c "..."` returns `python3`.
  */
 export function getCommandRoot(command: string): string | undefined {
   const trimmedCommand = command.trim();
@@ -301,22 +299,29 @@ export function getCommandRoot(command: string): string | undefined {
     return undefined;
   }
 
-  // This regex is designed to find the first "word" of a command,
-  // while respecting quotes. It looks for a sequence of non-whitespace
-  // characters that are not inside quotes.
-  const match = trimmedCommand.match(/^"([^"]+)"|^'([^']+)'|^(\S+)/);
-  if (match) {
-    // The first element in the match array is the full match.
-    // The subsequent elements are the capture groups.
-    // We prefer a captured group because it will be unquoted.
-    const commandRoot = match[1] || match[2] || match[3];
-    if (commandRoot) {
-      // If the command is a path, return the last component.
-      return commandRoot.split(/[\\/]/).pop();
+  try {
+    const tokens = parse(trimmedCommand).filter(
+      (token): token is string => typeof token === 'string',
+    );
+
+    let idx = 0;
+    while (idx < tokens.length && ENV_ASSIGNMENT_REGEX.test(tokens[idx]!)) {
+      idx++;
     }
-  }
 
-  return undefined;
+    const firstToken = tokens[idx];
+    return firstToken ? firstToken.split(/[\\/]/).pop() : undefined;
+  } catch {
+    const match = trimmedCommand.match(/^"([^"]+)"|^'([^']+)'|^(\S+)/);
+    if (match) {
+      const commandRoot = match[1] || match[2] || match[3];
+      if (commandRoot) {
+        return commandRoot.split(/[\\/]/).pop();
+      }
+    }
+
+    return undefined;
+  }
 }
 
 export function getCommandRoots(command: string): string[] {