I have used this code to compare two list which has million of records.
This method will not take much time
//Method to compare two list of string
private List<string> Contains(List<string> list1, List<string> list2)
{
List<string> result = new List<string>();
result.AddRange(list1.Except(list2, StringComparer.OrdinalIgnoreCase));
result.AddRange(list2.Except(list1, StringComparer.OrdinalIgnoreCase));
return result;
}