Disclosed in the present invention are a permanent magnet synchronous motor compensation control method and system. The method comprises: calculating a PI control output voltage VP of a permanent magnet synchronous motor (S102); performing disturbance observation on the permanent magnet synchronous motor, and calculating a disturbance compensation voltage VL of the permanent magnet synchronous motor (S104); calculating a repetitive control output voltage VR (S106); and on the basis of the PI control output voltage VP, the disturbance compensation voltage VL, and the repetitive control output voltage VR, obtaining a final output voltage Ve after current period compensation control (S108). According to the permanent magnet synchronous motor compensation control method, disturbance generated by three-phase imbalance is restrained by means of a disturbance observation voltage, steady-state errors of output signal control are reduced by means of a repetitive control voltage and a PI control output voltage, and when three-phase impedance changes during actual motor operation, the rotation speed and torque pulsation of the motor does not occur, such that normal operation of the motor is ensured, the system is stable, and the second-order harmonic amplitude caused by three-phase imbalance is effectively reduced.