This paper presents a torque ripple mitigation strategy for the fault tolerant permanent magnet synchronous motor (PMSM) drive system, in which an auxiliary phase is employed. It is shown that the torque ripple whose frequency is twice the fundamental frequency is induced in the PMSM undergoing an open circuit fault on a certain phase. In order to compensate the torque ripple, current controllers are implemented in the dual synchronous reference frame (SRF), in which the rotating frequencies of the two SRF are different. In more detail, one of the SRFs rotates in two times of the fundamental frequency to actively compensate the torque ripple in the steady state while another one is synchronized to the fundamental component. Compared to traditional methods, the proposed algorithm effectively extends the operating speed of the PMSM where the torque ripple can be compensated. Both the simulations and the experimental results confirm the usefulness of the proposed torque ripple mitigation strategy.