A method and apparatus for allocating a Peer-to-Peer (P2P) resource in a relay-based wireless communication system are provided. The method includes receiving relay link resource information, determining whether a current link is a multi-hop link by using the relay link resource information, and if the current link is the multi-hop link, allocating a corresponding relay link resource as the P2P resource by determining a serving station. Accordingly, P2P communication can be achieved without having to use additional P2P-dedicated resources.