1、保存sectionGroup到配置文件

/// <summary>
///  直接保存SectionGroup配置项
/// </summary>
public void SaveGroups()
{
    var configFilePath = AppDomain.CurrentDomain.SetupInformation.ConfigurationFile;//vs调试时，获取的配置文件是"文件名.vshost.exe.Config"，直接点击exe执行就正常了
    Console.WriteLine("configFilePath = " + configFilePath);
    var map = new ExeConfigurationFileMap { ExeConfigFilename = configFilePath };
    var config = ConfigurationManager.OpenMappedExeConfiguration(map, ConfigurationUserLevel.None);
    var root = new ConfigurationSectionGroup();
    config.SectionGroups.Add(ROOT_GROUP, root);
    config.Save(ConfigurationSaveMode.Modified);
    ConfigurationManager.RefreshSection(root.Name);
    var nested = new UserSettingsGroup();
    root.SectionGroups.Add(GROUP_1, nested);
    nested = new UserSettingsGroup();
    root.SectionGroups.Add(GROUP_2, nested);
    config.Save(ConfigurationSaveMode.Modified);
    ConfigurationManager.RefreshSection(root.Name);
}

配置文件中生成的配置项：

<sectionGroup name="ROOT_GROUP">
<sectionGroup name="GROUP_1" type="System.Configuration.UserSettingsGroup, System, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" >
</sectionGroup>
<sectionGroup name="GROUP_2" type="System.Configuration.ConfigurationSectionGroup, System.Configuration, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a" >
</sectionGroup>
</sectionGroup>

2、保存sectionGroup配置项之前删除之前存在的

/// <summary>
/// 保存之前，删除之前的SectionGroup配置项
/// </summary>
public void SaveGroup2()
{
    var configFilePath = AppDomain.CurrentDomain.SetupInformation.ConfigurationFile;//vs调试时，获取的配置文件是"文件名.vshost.exe.Config"，直接点击exe执行就正常了
    Console.WriteLine("configFilePath = " + configFilePath);
    var map = new ExeConfigurationFileMap { ExeConfigFilename = configFilePath };
    var config = ConfigurationManager.OpenMappedExeConfiguration(map, ConfigurationUserLevel.None);
    var root = config.SectionGroups[ROOT_GROUP];
    var existingGroups = new Dictionary<string, ConfigurationSectionGroup>();
    while (root.SectionGroups.Count > 0)
    {
    existingGroups.Add(root.SectionGroups.Keys[0], root.SectionGroups[0]);
    root.SectionGroups.RemoveAt(0);
    }
    config.Save(ConfigurationSaveMode.Modified);
    existingGroups.Clear();
    existingGroups.Add(GROUP_2, new UserSettingsGroup());
    foreach (var key in existingGroups.Keys)
    {
    existingGroups[key].ForceDeclaration(true);
    root.SectionGroups.Add(key, existingGroups[key]);
    }
    config.Save(ConfigurationSaveMode.Modified);
    ConfigurationManager.RefreshSection(root.Name);
}

配置文件中生成的配置项：

<sectionGroup name="ROOT_GROUP">
<sectionGroup name="GROUP_2" type="System.Configuration.UserSettingsGroup, System, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" >
</sectionGroup>
</sectionGroup>

3、测试项目代码

using System;
using System.Collections.Generic;
using System.Configuration;
using System.Linq;
using System.Text;
using System.Threading.Tasks;
namespace ConsoleApplication1
{
    class Program
    {
        static void Main(string[] args)
        {
            var a = new ConfigUtil();
            a.SaveGroups();
            a.SaveGroup2();    
            Console.ReadKey();
        }
    }
    public class ConfigUtil
    {
        private string ROOT_GROUP = "ROOT_GROUP";
        private string GROUP_1 = "GROUP_1";
        private string GROUP_2 = "GROUP_2";
        private Configuration GetConfig()
        {
            var configFilePath = AppDomain.CurrentDomain.SetupInformation.ConfigurationFile;//vs调试时，获取的配置文件是"文件名.vshost.exe.Config"，直接点击exe执行就正常了
            Console.WriteLine("configFilePath = " + configFilePath);
            var map = new ExeConfigurationFileMap { ExeConfigFilename = configFilePath };
            var config = ConfigurationManager.OpenMappedExeConfiguration(map, ConfigurationUserLevel.None);
            return config;
        }
        /// <summary>
        ///  直接保存SectionGroup配置项
        /// </summary>
        public void SaveGroups()
        {
            var config = GetConfig();
            var root = new ConfigurationSectionGroup();
            config.SectionGroups.Add(ROOT_GROUP, root);
            config.Save(ConfigurationSaveMode.Modified);
            ConfigurationManager.RefreshSection(root.Name);
            var nested = new UserSettingsGroup();
            root.SectionGroups.Add(GROUP_1, nested);
            nested = new UserSettingsGroup();
            root.SectionGroups.Add(GROUP_2, nested);
            config.Save(ConfigurationSaveMode.Modified);
            ConfigurationManager.RefreshSection(root.Name);
        }
        /// <summary>
        /// 保存之前，删除之前的SectionGroup配置项
        /// </summary>
        public void SaveGroup2()
        {
            var config = GetConfig();
            var root = config.SectionGroups[ROOT_GROUP];
            var existingGroups = new Dictionary<string, ConfigurationSectionGroup>();
            while (root.SectionGroups.Count > 0)
            {
                existingGroups.Add(root.SectionGroups.Keys[0], root.SectionGroups[0]);
                root.SectionGroups.RemoveAt(0);
            }
            config.Save(ConfigurationSaveMode.Modified);
            existingGroups.Clear();
            existingGroups.Add(GROUP_2, new UserSettingsGroup());
            foreach (var key in existingGroups.Keys)
            {
                existingGroups[key].ForceDeclaration(true);
                root.SectionGroups.Add(key, existingGroups[key]);
            }
            config.Save(ConfigurationSaveMode.Modified);
            ConfigurationManager.RefreshSection(root.Name);
        }
    }
}