For the problem that five-phase permanent magnet synchronous motor inter-turn short-circuit fault and high resistance connection fault have the same fault characteristics, a fault detection and classification method based on current residual estimation and high-frequency current comparison is proposed. Firstly, the Kalman filter is used to detect the abnormal condition of motor by estimating the current residual of d-q axis during fault. Then the different characteristics of inductance and resistance at high frequency are used to distinguish the inter-turn short-circuit fault and high resistance connection fault. Finally, the severity and faulty phase of the two faults are studied. Simulation results show that this method can effectively diagnose motor stator faults and accurately identify inter-turn short-circuit fault and high resistance connection fault, and the severity of the fault has good robustness against the change of speed and load.