Why does Booth called Dr. Brennan Bones? Is it a part of her real name or a nickname?

It's a nickname. :) He calls her Bones because she's a forensic anthropologist and works with bones.

The first answer is of course correct as anyone would expect. But something that has been overlooked about this show from the start is that they come up with answers as to cause of death and even suspects from looking at bones and now even using holograms that can't exist to determine things that can't be done with bones alone in most cases.

Booth just decided to call her that.. she didnt like it at first and kept trying to get him to stop, but he just ignored her and it stuck..