Analyzes the shortcomings of traditional power system protection method and introduces the principle of intelligent protection method based on BP neural network. In order to verify the validity and correctness of the method, constructs the power system simulation model based on the PSCAD/EMTDC, and with two phase current RMS and three phase current maximum value as neural network input respectively, conducts a simulation study and comparative analysis. The result shows that the intelligent protection method based on BP neural network for ship power system fault locating is accurate and feasible, and the maximum three-phase current input signals as the input signal of intelligent protection have more advantages.