Like any desk, it is used primarily for official use, as well as doing work. The drawers are used as storage locations, keeping items handy for easy retrieval, or reference. On the top, one will find all the things might expect to find in an office. A desk lamp, recording device, and a phone also adorn the desk.
In the course of the game, the desk is found to be the hiding spot of the Ash Talisman. Most likely hidden there by the Professor to help anyone he had found to help. It is an easy enough space to discover, since when most people search desks, they open every drawer possible.