Is there any branch change in IIITs?

This depends on the management of that particular college, as IIIT, Pune allows branch change but IIIT, Ranchi doesn't.

Yes, It all depends on the branch strength. All you need to do is get a good score in CSE subjects (to prove that you'll be well suited in CSE) and score good in ECE subjects (to prove that you didn't score well in CS courses at the cost of EC courses) You have to get equally good scores in subjects