I am thinking to change the colour schema in my one of the main site and I am sure it will helpful for getting more CTR, but increase in CTR will make any problem as there will not be much difference in traffic ? Or do I mail google first ?
Just change your color scheme - you don't need approval from Google to do that. If your CTR increases that's great. Google is not going to kick you out because your CTR went up, and I'd be surprised if it went up enough for Google to notice anyway. I've changed color schemes a couple of times and seen minor increases.