diff --git a/src/commands/set.ts b/src/commands/set.ts
index a3dff37..87d5218 100644
--- a/src/commands/set.ts
+++ b/src/commands/set.ts
@@ -3,7 +3,7 @@ import chalk from 'chalk';
 import { existsSync } from 'fs';
 import { join } from 'path';
 import { ConfigManager } from '@/utils/config';
-import { saveEnvs, writeEnvs } from '@/utils/com';
+import { getEnvs, saveEnvs, writeEnvs } from '@/utils/com';
 import { EnvConfig } from '@/types/config';
 import { 
   validateEnvKey, 
@@ -17,6 +17,7 @@ export function setCommand(program: Command): void {
     .option('-c, --config <path>', 'Path to config file (default: ./envx.config.yaml)', './envx.config.yaml')
     .option('-d, --description <text>', 'Description for the environment variable')
     .option('-t, --target <path>', 'Target path for the environment variable')
+    .option('--files <paths>', 'Target file paths for monorepo (comma-separated, e.g. apps/web/.env,apps/api/.env)')
     .option('--force', 'Force update without confirmation if variable exists')
     .action(async (key: string, value: string, options) => {
       try {
@@ -81,6 +82,11 @@ export function setCommand(program: Command): void {
           envConfig.target = options.target;
         }
 
+        if (options.files) {
+          const filesList = options.files.split(',').map((f: string) => f.trim());
+          envConfig.files = filesList.length === 1 ? filesList[0] : filesList;
+        }
+
         // 更新配置
         configManager.setEnvVar(key, envConfig);
         configManager.save();
@@ -89,11 +95,13 @@ export function setCommand(program: Command): void {
         console.log(chalk.blue('🗄️  Updating database...'));
         await saveEnvs(configPath, { [key]: value }, 'default');
 
-        // 写入环境文件（writeEnvs）
+        // 写入环境文件（writeEnvs）— 读取完整环境后合并写入，避免覆盖其他变量
         if (config.files) {
           console.log(chalk.blue('🔄 Updating environment file based on clone configuration...'));
           try {
-            await writeEnvs(configPath, { [key]: value });
+            const currentEnvs = await getEnvs(configPath);
+            currentEnvs[key] = value;
+            await writeEnvs(configPath, currentEnvs);
             console.log(chalk.green('✅ Environment file updated'));
           } catch (error) {
             console.warn(
@@ -121,6 +129,10 @@ export function setCommand(program: Command): void {
         if (options.target) {
           console.log(chalk.gray(`   Target: ${options.target}`));
         }
+
+        if (options.files) {
+          console.log(chalk.gray(`   Files: ${options.files}`));
+        }
         
         // 显示配置相关信息
         if (isEnvRequired(key, config)) {
diff --git a/src/utils/com.ts b/src/utils/com.ts
index 279d508..c61ffda 100644
--- a/src/utils/com.ts
+++ b/src/utils/com.ts
@@ -7,16 +7,15 @@ import { dirname, isAbsolute, join } from 'path';
 export async function getEnvs(configPath: string, tag?: string): Promise<EnvMap> {
   const configManager = new ConfigManager(configPath);
   const isExport = configManager.isExport();
-  const files = configManager.getEnvFilesConfig();
+  const globalFiles = configManager.getEnvFilesConfig();
+  const configDir = dirname(configPath);
 
   // 允许键集合来自配置文件定义
   const configKeys = Object.keys(configManager.getConfig().env);
+  const allConfigs = configManager.getAllEnvConfigs();
 
   let envMap: EnvMap = {};
 
-  // 数据库目录应为配置文件所在目录
-  const configDir = dirname(configPath);
-
   if (tag) {
     const dbManager = createDatabaseManagerFromConfigPath(configPath);
     try {
@@ -27,23 +26,48 @@ export async function getEnvs(configPath: string, tag?: string): Promise<EnvMap>
     }
   }
 
-  // 合并 .env 文件内容
-  for (const file of files) {
+  // 收集所有需要读取的文件
+  const allFiles = new Set<string>(globalFiles);
+  for (const conf of allConfigs) {
+    if (conf.config.files) {
+      const files = Array.isArray(conf.config.files) ? conf.config.files : [conf.config.files];
+      files.forEach(f => allFiles.add(f));
+    }
+  }
+
+  // 读取所有相关文件到缓存
+  const fileContents: Record<string, EnvMap> = {};
+  for (const file of allFiles) {
     const filePath = isAbsolute(file) ? file : join(configDir, file);
-    const fileEnvs = await readEnvFile(filePath);
-    envMap = mergeEnv(envMap, fileEnvs, true);
+    fileContents[file] = await readEnvFile(filePath);
+  }
+
+  // 按变量从其配置的目标文件中读取值
+  for (const conf of allConfigs) {
+    const key = conf.key;
+    let targetFiles: string[];
+    if (conf.config.files) {
+      targetFiles = Array.isArray(conf.config.files) ? conf.config.files : [conf.config.files];
+    } else {
+      targetFiles = globalFiles;
+    }
+
+    for (const file of targetFiles) {
+      const fileEnv = fileContents[file];
+      if (fileEnv && key in fileEnv) {
+        envMap[key] = fileEnv[key];
+      }
+    }
   }
 
   // 如果开启 export，则从当前进程环境中读取并合并（仅限已定义键）
   if (isExport) {
-    const processingEnv: EnvMap = {};
     for (const key of configKeys) {
       const val = process.env[key];
       if (val !== undefined) {
-        processingEnv[key] = String(val);
+        envMap[key] = String(val);
       }
     }
-    envMap = mergeEnv(envMap, processingEnv, true);
   }
 
   // 只保留配置里声明过的键
@@ -68,10 +92,37 @@ export async function saveEnvs(configPath: string, envMap: EnvMap, tag?: string)
 
 export async function writeEnvs(configPath: string, envMap: EnvMap) {
   const configManager = new ConfigManager(configPath);
-  const files = configManager.getEnvFilesConfig();
+  const globalFiles = configManager.getEnvFilesConfig();
   const configDir = dirname(configPath);
-  for (const file of files) {
+  const allConfigs = configManager.getAllEnvConfigs();
+
+  // 按目标文件分组变量
+  const fileEnvMap: Record<string, EnvMap> = {};
+  for (const file of globalFiles) {
+    fileEnvMap[file] = {};
+  }
+
+  for (const [key, value] of Object.entries(envMap)) {
+    const envConf = allConfigs.find(c => c.key === key);
+    let targetFiles: string[];
+
+    if (envConf?.config.files) {
+      targetFiles = Array.isArray(envConf.config.files)
+        ? envConf.config.files
+        : [envConf.config.files];
+    } else {
+      targetFiles = globalFiles; // fallback 到全局 files
+    }
+
+    for (const file of targetFiles) {
+      if (!fileEnvMap[file]) fileEnvMap[file] = {};
+      fileEnvMap[file][key] = value;
+    }
+  }
+
+  // 按文件写入
+  for (const [file, envs] of Object.entries(fileEnvMap)) {
     const filePath = isAbsolute(file) ? file : join(configDir, file);
-    await writeEnvFile(filePath, envMap);
+    await writeEnvFile(filePath, envs);
   }
 }
diff --git a/src/utils/config/config-validator.ts b/src/utils/config/config-validator.ts
index 8086003..165a76e 100644
--- a/src/utils/config/config-validator.ts
+++ b/src/utils/config/config-validator.ts
@@ -151,13 +151,20 @@ export class ConfigValidator {
               }
             }
 
-            // 检查路径冲突（仅在全局与局部都为字符串时检查完全相等）
-            if (
-              typeof config.files === 'string' &&
-              typeof envConfig.files === 'string' &&
-              envConfig.files === config.files
-            ) {
-              warnings.push(`环境变量 "${key}" 的 clone 路径与全局 clone 路径相同，可能造成冲突`);
+            // 检查 per-variable files 是否为全局 files 的子集
+            const globalFilesList = config.files
+              ? (Array.isArray(config.files) ? config.files : [config.files])
+              : [];
+            const varFilesList = Array.isArray(envConfig.files)
+              ? envConfig.files
+              : [envConfig.files];
+
+            for (const vf of varFilesList) {
+              if (globalFilesList.length > 0 && !globalFilesList.includes(vf)) {
+                warnings.push(
+                  `环境变量 "${key}" 的目标文件 "${vf}" 未在全局 files 中声明`
+                );
+              }
             }
           }
         }
diff --git a/src/utils/env/index.ts b/src/utils/env/index.ts
index b094e96..cc7aea8 100644
--- a/src/utils/env/index.ts
+++ b/src/utils/env/index.ts
@@ -1,4 +1,5 @@
 import { promises as fs } from 'fs';
+import { dirname } from 'path';
 import { EnvxConfig } from '@/types/config';
 import { EnvMap, ShellKind } from '@/types/common';
 import { spawn } from 'child_process';
@@ -65,6 +66,8 @@ export async function readEnvFile(filePath: string): Promise<EnvMap> {
  */
 export async function writeEnvFile(filePath: string, env: EnvMap): Promise<void> {
   const output = serializeEnv(env);
+  const dir = dirname(filePath);
+  await fs.mkdir(dir, { recursive: true });
   await fs.writeFile(filePath, output, 'utf8');
 }