Abstract: The multi-phase permanent magnet synchronous motor drive system has strong fault-tolerant operation ability. The non-sinusoidal back-EMF five-phase permanent magnet synchronous motor is taken as the research object. By adopting the reduced order transformation matrix, the torque equations at fundamental and the third harmonic space are constructed under the single-phase fault. And in order to eliminate the second and fourth torque ripples under the fault, the method of selecting the third harmonic current injection rate is analyzed, and the reference current are optimized according to the principle of minimum copper loss and maximum torque. In addition, to address the inability of traditional PI controller to track the AC reference current in an accurate way, a Quasi-proportional resonance (QPR) +PI controller is designed on the basis of PI control to ensure the accuracy in tracking the AC reference current in the synchronous coordinate system. The simulation results demonstrate that the torque ripple are effectively suppressed, and the QPR + PI controller can accurately track the AC current signal.