With the development of ship integrated power system, the configuration, network structure and operation mode of it have been greatly changed. As a result, the traditional ship relay protection methods can not meet the needs of the system any longer. In this paper, the fault characteristic signals of ship integrated power system are analyzed. An intelligent relay protection method based on Transfer Support Vector Machine (TrSVM) is proposed. The mathematical model is derived and the simulation model is constructed in PSCAD/EMTDC software for comparative analysis to verify the proposed method. Finally, the results validate that the method in this paper is able to deal with the complex fault situation in the complex ship integrated power system and meet the relay protection. This work is supported by National Natural Science Foundation of China (No. 51377167).