Which question is best if want to know what a student's opinion is about the things he is doing at university?


'What do you think of your study?'

or

'what do you think of your studies?'


What is the difference?

Studies. Simply a convention based, I guess, on the fact that it is the plural of study and the student will be doing a lot of studying. But if you are asking a question about the whole university experience, rather than just their studies, then ask them just that, i.e. what do they think of their university experience.

One last thing: I should make it clear that I think the words 'study' and 'studies' are nouns in this instance, rather than verbs.

They are indeed nouns.