Mohit, 

Yes you need to pay INR 10000+1000 equals to INR 11000 when you apply for Chandigarh University. 

They take it as security or you may say seat freezing money .

It is taken by most of the colleges in India to ensure that you don't cancel your seat after college begins.  If you do so their college seat is wasted which might have been allotted to someone else. 

But you can cancel seat in Chandigarh University before 10 th of July they just deduct INR 1000 and you will get back INR 10000.

HOPE IT HELPS