What is the difference between Periodic and Non-Periodic Tx/Rx FIFO in USB?
The reference manual where you found these terms mentioned itself explains that the two types of FIFOs are used for different types of USB transfers, for example in section 34.12.2


  The host uses one transmit FIFO for all non-periodic (control and bulk) OUT transactions and one transmit FIFO for all periodic (isochronous and interrupt) OUT transactions.


Realistically you probably should not be looking at the hardware engine in this level of detail unless you have substantial USB expertise; for any normal use you would let an existing USB stack (from ST or someone else) handle it, and only worry about following the requirements/examples for integration and providing or claiming data with the appropriate APIs.  Getting this level of detail would tend to occur only if trying to write your own USB stack or if trying to de behind-the-scenes debugging of an unexpected incompatibility.