每个AppDomain都有/可以有自己的配置文件。CLR主机创建的默认AppDomain使用programname.exe.config。如果要提供自己的配置文件，请创建单独的AppDomain。例：

// get the name of the assembly
string exeAssembly = Assembly.GetEntryAssembly().FullName;

// setup - there you put the path to the config file
AppDomainSetup setup = new AppDomainSetup();
setup.ApplicationBase = System.Environment.CurrentDirectory;
setup.ConfigurationFile = "<path to your config file>";

// create the app domain
AppDomain appDomain = AppDomain.CreateDomain("My AppDomain", null, setup);

// create proxy used to call the startup method 
YourStartupClass proxy = (YourStartupClass)appDomain.CreateInstanceAndUnwrap(
       exeAssembly, typeof(YourStartupClass).FullName);

// call the startup method - something like alternative main()
proxy.StartupMethod();

// in the end, unload the domain
AppDomain.Unload(appDomain);

希望能有所帮助。