The invention discloses a method and a system for identifying application traffic of a peer-to-peer network. The method comprises the following steps: acquiring all data packets by a detecting device; filtering the data packets primarily; performing plaintext characteristic string detection of known P2P application on the filtered data packets; sending the data packets into a P2P processing module after adding a plaintext identification or a ciphertext identification to the data packets correspondingly; respectively searching the data packets which comprise the plaintext identification and the ciphertext identification; counting P2P traffic transmitted in a mode of plaintext or ciphertext; for an unmatched ciphertext data packet, constructing an active detecting data packet to be transmitted to a detected target; and identifying the P2P traffic transmitted in the mode of the ciphertext or other unknown traffic according to a response data packet replied by the detected target. The technical scheme provided by the invention can effectively reduce processing workload of traffic detection, and improve the efficiency of the system; and a fault and the updating of a single module do not influence the overall system. The technology has no influence on the topology and the performance of the conventional network, and is convenient to deploy and implement.