Skype is a P2P overlay network for VoIP and other applications, which is widely used all over the world. Based on analysis of the operation mechanisms, the communication processes of Skype are discussed detailedly, and then a multiple-layer based system for Skype network traffic identification is designed. The System mainly consists of three entities, which include suspicious connection table, payload detection module and traffic detection module. The functional characteristics of all entities are introduced, and the attribute set for network behavior is depicted. Finally, experiment results show the usability of the system.