要实现Asp.Net Core 3.1中多个依赖的自定义配置提供程序，可以按照以下步骤进行：

1. 创建一个名为CustomConfigurationProvider的自定义配置提供程序。

public class CustomConfigurationProvider : ConfigurationProvider
{
    private readonly Action _configureSource;

    public CustomConfigurationProvider(Action configureSource)
    {
        _configureSource = configureSource;
    }

    public override void Load()
    {
        var source = new CustomConfigurationSource();
        _configureSource(source);

        Data = source.Data;
    }
}

2. 创建一个名为CustomConfigurationSource的自定义配置源。

public class CustomConfigurationSource : IConfigurationSource
{
    public IDictionary Data { get; set; }

    public IConfigurationProvider Build(IConfigurationBuilder builder)
    {
        return new CustomConfigurationProvider(configureSource =>
        {
            configureSource.Data = Data;
        });
    }
}

3. 在Startup.cs文件的ConfigureServices方法中注册自定义配置提供程序。

public void ConfigureServices(IServiceCollection services)
{
    services.AddSingleton(provider =>
    {
        var data1 = new Dictionary
        {
            {"Key1", "Value1"},
            {"Key2", "Value2"}
        };

        var data2 = new Dictionary
        {
            {"Key3", "Value3"},
            {"Key4", "Value4"}
        };

        var config1 = new ConfigurationBuilder()
            .Add(new CustomConfigurationSource { Data = data1 })
            .Build();

        var config2 = new ConfigurationBuilder()
            .Add(new CustomConfigurationSource { Data = data2 })
            .Build();

        return new ConfigurationBuilder()
            .AddConfiguration(config1)
            .AddConfiguration(config2)
            .Build();
    });

    // 其他服务配置
}

4. 在需要使用配置的地方注入IConfiguration依赖，并使用GetSection方法来获取配置值。

public class HomeController : Controller
{
    private readonly IConfiguration _configuration;

    public HomeController(IConfiguration configuration)
    {
        _configuration = configuration;
    }

    public IActionResult Index()
    {
        var value1 = _configuration.GetSection("Key1").Value;
        var value2 = _configuration.GetSection("Key2").Value;
        var value3 = _configuration.GetSection("Key3").Value;
        var value4 = _configuration.GetSection("Key4").Value;

        // 其他操作

        return View();
    }
}

通过以上步骤，就可以实现在Asp.Net Core 3.1中使用多个依赖的自定义配置提供程序了。