Hi,

Courses.

Almost all the CS courses are taught in MnC department but there’s a difference. Mnc courses are more inclined towards Mathematics and not much coding. It is you who will have to code. The professors in MnC department won’t pay much heed.  

CS department will give you lots of program to code. Coding will become your cup of coffee. 

Interests.

Mathematics is all different after coming to IIT. Rather than solving skills you will need more of mugging up. I have seen many of my friends lose their interest in Mathematics after joining. I’m not trying to intimidate you but Mathematics here is indeed different from that of your school days.

If you are interested in both subjects, more in CS, go for the CS department. You can always take additional courses in MnC department to satiate your desire for Maths.