With the development of the industrial ethernet, the clock synchronization protocol which is the core technology of industrial ethernet real-time has become crucial. For the problem of the clock synchronization protocol security, a method for analyzing the clock synchronization protocol security using colored Petri net is proposed. Firstly, the protocol is modeled by using colored Petri net. Then the reachability of possible insecurity state is judged and analyzed by using the model through state equation, thus the security analysis of the clock synchronization protocol is realized. Finally, a clock synchronization protocol based on PTP and the main-clock spoofing attack aiming at this protocol are analyzed by using this method, and the result shows the effectiveness of the proposed method.