diff --git a/agent/shell_hooks.py b/agent/shell_hooks.py
index 5292244e2..c1cec81df 100644
--- a/agent/shell_hooks.py
+++ b/agent/shell_hooks.py
@@ -224,6 +224,15 @@ def register_from_config(
     if not isinstance(cfg, dict):
         return []
 
+    # Safe mode (--safe-mode / HERMES_SAFE_MODE=1): shell hooks are user
+    # customizations too — skip registration entirely so a troubleshooting
+    # run fires zero user-configured code (plugins, MCP, AND hooks).
+    from utils import env_var_enabled
+
+    if env_var_enabled("HERMES_SAFE_MODE"):
+        logger.info("HERMES_SAFE_MODE=1 — shell-hook registration skipped")
+        return []
+
     effective_accept = _resolve_effective_accept(cfg, accept_hooks)
 
     specs = _parse_hooks_block(cfg.get("hooks"))
diff --git a/tests/hermes_cli/test_safe_mode.py b/tests/hermes_cli/test_safe_mode.py
index 6ab0cf533..ffd0b85b8 100644
--- a/tests/hermes_cli/test_safe_mode.py
+++ b/tests/hermes_cli/test_safe_mode.py
@@ -130,3 +130,40 @@ def test_parser_accepts_safe_mode_on_root_and_chat():
     assert parser.parse_args(["--safe-mode"]).safe_mode is True
     assert parser.parse_args(["chat", "--safe-mode"]).safe_mode is True
     assert parser.parse_args(["chat"]).safe_mode is False
+
+
+def test_shell_hooks_skipped(monkeypatch):
+    monkeypatch.setenv("HERMES_SAFE_MODE", "1")
+    from agent.shell_hooks import register_from_config
+
+    cfg = {
+        "hooks": {
+            "pre_tool_call": [{"command": "echo hooked"}],
+        },
+        "hooks_auto_accept": True,
+    }
+
+    assert register_from_config(cfg, accept_hooks=True) == []
+
+
+def test_shell_hooks_register_without_safe_mode(monkeypatch):
+    import agent.shell_hooks as sh
+
+    cfg = {
+        "hooks": {
+            "pre_tool_call": [{"command": "echo hooked"}],
+        },
+        "hooks_auto_accept": True,
+    }
+
+    manager = types.SimpleNamespace(_hooks={})
+    plugins = types.ModuleType("hermes_cli.plugins")
+    setattr(plugins, "get_plugin_manager", lambda: manager)
+    setattr(plugins, "VALID_HOOKS", {"pre_tool_call"})
+    monkeypatch.setitem(sys.modules, "hermes_cli.plugins", plugins)
+    monkeypatch.setattr(sh, "_registered", set())
+
+    registered = sh.register_from_config(cfg, accept_hooks=True)
+
+    assert len(registered) == 1
+    assert "pre_tool_call" in manager._hooks
diff --git a/website/docs/reference/cli-commands.md b/website/docs/reference/cli-commands.md
index 1bc4d4b13..b8ace5b19 100644
--- a/website/docs/reference/cli-commands.md
+++ b/website/docs/reference/cli-commands.md
@@ -117,7 +117,7 @@ Common options:
 | `--pass-session-id` | Pass the session ID into the system prompt. |
 | `--ignore-user-config` | Ignore `~/.hermes/config.yaml` and use built-in defaults. Credentials in `.env` are still loaded. Useful for isolated CI runs, reproducible bug reports, and third-party integrations. |
 | `--ignore-rules` | Skip auto-injection of `AGENTS.md`, `SOUL.md`, `.cursorrules`, persistent memory, and preloaded skills. Combine with `--ignore-user-config` for a fully isolated run. |
-| `--safe-mode` | Troubleshooting mode: disable ALL customizations — user config, rules/memory injection, plugins, and MCP servers (implies `--ignore-user-config` and `--ignore-rules`). Use to isolate whether a problem comes from your setup or from Hermes itself. |
+| `--safe-mode` | Troubleshooting mode: disable ALL customizations — user config, rules/memory injection, plugins, shell hooks, and MCP servers (implies `--ignore-user-config` and `--ignore-rules`). Use to isolate whether a problem comes from your setup or from Hermes itself. |
 | `--source <tag>` | Session source tag for filtering (default: `cli`). Use `tool` for third-party integrations that should not appear in user session lists. |
 | `--max-turns <N>` | Maximum tool-calling iterations per conversation turn (default: 90, or `agent.max_turns` in config). |
 
diff --git a/website/docs/reference/environment-variables.md b/website/docs/reference/environment-variables.md
index 9f4aa2144..9e95d90e3 100644
--- a/website/docs/reference/environment-variables.md
+++ b/website/docs/reference/environment-variables.md
@@ -716,7 +716,7 @@ Advanced per-platform knobs for throttling the outbound message batcher. Most us
 | `HERMES_ACCEPT_HOOKS` | Auto-approve any unseen shell hooks declared in `config.yaml` without a TTY prompt. Equivalent to `--accept-hooks` or `hooks_auto_accept: true`. |
 | `HERMES_IGNORE_USER_CONFIG` | Skip `~/.hermes/config.yaml` and use built-in defaults (credentials in `.env` still load). Equivalent to `--ignore-user-config`. |
 | `HERMES_IGNORE_RULES` | Skip auto-injection of `AGENTS.md`, `SOUL.md`, `.cursorrules`, memory, and preloaded skills. Equivalent to `--ignore-rules`. |
-| `HERMES_SAFE_MODE` | Troubleshooting mode: disable ALL customizations — skips plugin discovery and MCP server loading. Set automatically by `--safe-mode` (which also sets the two flags above). |
+| `HERMES_SAFE_MODE` | Troubleshooting mode: disable ALL customizations — skips plugin discovery, MCP server loading, and shell-hook registration. Set automatically by `--safe-mode` (which also sets the two flags above). |
 | `HERMES_MD_NAMES` | Comma-separated list of rules-file names to auto-inject (default: `AGENTS.md,CLAUDE.md,.cursorrules,SOUL.md`). |
 | `HERMES_TOOL_PROGRESS` | Deprecated compatibility variable for tool progress display. Prefer `display.tool_progress` in `config.yaml`. |
 | `HERMES_TOOL_PROGRESS_MODE` | Deprecated compatibility variable for tool progress mode. Prefer `display.tool_progress` in `config.yaml`. |
diff --git a/website/i18n/zh-Hans/docusaurus-plugin-content-docs/current/reference/environment-variables.md b/website/i18n/zh-Hans/docusaurus-plugin-content-docs/current/reference/environment-variables.md
index 7ee79f765..8de0ad1a9 100644
--- a/website/i18n/zh-Hans/docusaurus-plugin-content-docs/current/reference/environment-variables.md
+++ b/website/i18n/zh-Hans/docusaurus-plugin-content-docs/current/reference/environment-variables.md
@@ -532,7 +532,7 @@ Graph 事件（Teams 会议、日历、聊天等）的入站变更通知监听
 | `HERMES_ACCEPT_HOOKS` | 无需 TTY 提示自动批准 `config.yaml` 中声明的任何未见过的 shell hook。等同于 `--accept-hooks` 或 `hooks_auto_accept: true`。 |
 | `HERMES_IGNORE_USER_CONFIG` | 跳过 `~/.hermes/config.yaml` 并使用内置默认值（`.env` 中的凭证仍会加载）。等同于 `--ignore-user-config`。 |
 | `HERMES_IGNORE_RULES` | 跳过 `AGENTS.md`、`SOUL.md`、`.cursorrules`、记忆和预加载技能的自动注入。等同于 `--ignore-rules`。 |
-| `HERMES_SAFE_MODE` | 故障排查模式：禁用**所有**自定义项——跳过插件发现和 MCP 服务器加载。由 `--safe-mode` 自动设置（同时也会设置上面两个 flag）。 |
+| `HERMES_SAFE_MODE` | 故障排查模式：禁用**所有**自定义项——跳过插件发现、MCP 服务器加载和 shell hook 注册。由 `--safe-mode` 自动设置（同时也会设置上面两个 flag）。 |
 | `HERMES_MD_NAMES` | 自动注入的规则文件名逗号分隔列表（默认：`AGENTS.md,CLAUDE.md,.cursorrules,SOUL.md`）。 |
 | `HERMES_TOOL_PROGRESS` | 工具进度显示的已弃用兼容变量。优先使用 `config.yaml` 中的 `display.tool_progress`。 |
 | `HERMES_TOOL_PROGRESS_MODE` | 工具进度模式的已弃用兼容变量。优先使用 `config.yaml` 中的 `display.tool_progress`。 |