1. On the 2nd basement, there is a book store.

2. In the 2nd basement, there is a book store.
3. A book store is on the 2nd basement.
4. A book store is in the 2nd basement.
5. A book store is on basement 2.
6. A book store is in basement 2.
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Which one is correct? Do we have to use 'in' or 'on'?

2, 4, and 6 are correct.

Be sure you remember the difference between "in" (inside) and "on" (on top of).