How to remove same combination (same number but diffrent order) on list?

A quick and a bit dirty way of getting what you wanted, without custom comparer and with items in original order:

using System;
using System.Collections.Generic;
using System.Linq;

public class Program
{
    public static void Main()
    {
        List<string> MyList = new List<string>();
        MyList.Add("153");
        MyList.Add("112");
        MyList.Add("531");
        MyList.Add("675");
        MyList.Add("889");
        MyList.Add("351");
        
        int i = 0;
        var ac = new Dictionary<int, string>();
        var res = new Dictionary<int, string>(); 

        foreach (var a in MyList)
        {
            res.Add(i, a);
            var ou = a.ToArray();
            Array.Sort(ou);
            ac.Add(i, new String(ou));
            i++;
        }

        var filteredDictionary = ac.GroupBy(s => s.Value).Where(gr => gr.Any()).Select(g => g.First()).ToDictionary(kvp => kvp.Key, kvp => kvp.Value);
        var ret = res.Where(x => filteredDictionary.ContainsKey(x.Key)).Select(x => x.Value);
        foreach (var c in ret)
        {
            Console.WriteLine(c);
        }
    }
}

Result:

153
112
675
889

Fiddle: https://dotnetfiddle.net/#&togetherjs=1dgVkP8AGf

This does not contain any safety checks, nor does it handle strings that are not 'numbers', but will work with your example leaving first occurrence of given combination.