Faulttolerant permanent magnet motor (FTPMM) combines the merits of permanent magnet synchronous motor and switch reluctance motor, so it can be used as the propulsion motor of electric propulsion ship. On the basis of analyzing the structure and mathematical model of FTPMM, the fuzzy adaptive PI control strategy was proposed. During the control process, if the error was large, the control weight of error would be increased so as to improve the response speed; if the error was small, the control weight of the change of error would be raised, so that the system could reach the steady state as soon as possible. The simulation model of electric propulsion ship system using the fuzzy adaptive PI control strategy in propulsion motor was built in MATLAB/simulink. From the simulation results, it was proved that the dynamic and static properties of FTPMM were improved in comparison with the traditional PI control, and the fuzzy adaptive PI control was suitable for the application in marine electric propulsion system.