Hi, This is the common query students have between these 2 branches. CS is mostly about understanding the inner workings and concepts behind programming and computers whereas IT is more about applying these concepts in real life.

Differences:
The CS engineering programme usually deals with how to build microprocessors, how to write a compiler etc. IT is the business side of computers - usually dealing with databases, business, and accounting. One way to think of it is that IT deals with the application of computing technology to real life processes and CSE deals with the science that facilitates these applications. 
If you have to choose between IT and CSE and have both options in hand, it would be wise to decide it on the basis of the reputation and standing of the college rather than the branch. If you have to choose between IT and CSE in the same college, see what excites you more, design of computers and computing systems or using computers to solve information management requirements of organisation.

To explain it well I am sharing you a link which describes it all.
Link: http://www.engineering.careers360.com/articles/Engineering-branches-Comp-Science-Vs-IT
This shall help you.
Good Luck.