Based on fluctuating high frequency voltage signal injection sensorless control method, position sensor fault-tolerant control system for permanent magnet synchronous motor (PMSM) was designed. The phase delay, which existed between high frequency current signal and demodulated signal, was analyzed. The phase delay was caused by the inverter, the stator resistance and AD sampling time. The effect of the mutual inductance and the harmonic inductance on position estimation error were analyzed. And a compensation method was proposed. Simulation and experiment results showed that the position sensor fault-tolerant control system had the advantage of high tracking accuracy and certain disturbance-rejecting ability. It had also a good speed and position estimation performance at zero and low speed. 