Compared with the traditional permanent magnet motor, the non-sinusoidal back-EMF permanent magnet motor can improve the torque density but when the motor fails, the back-EMF harmonics will produce torque ripple during the fault tolerance process. In this paper, the mathematical model of non-sinusoidal back-EMF motor is given and the torque ripple before and after fault is deduced. Based on the three-phase four-leg topology, a fault-tolerant control strategy for the open-phase fault of permanent magnet synchronous motor (PMSM) with the introduction of the third and fifth harmonic back-EMF is proposed in order to weaken the torque ripple caused by the introduced back-EMF harmonics. Finally, the effectiveness of the proposed control strategy is verified by simulation.