Multi-phase motors and generators are regarded with great fault tolerance capability, especially on open-circuit faults. Various mathematics analytical methods are applied for their fault control. In this paper, a fault-tolerant control strategy with asymmetric phase current for the open-circuit faults with arbitrary phases in the six-phase PMSM (six-phase permanent magnetic synchronous motor, 6P-PMSM) system, is proposed for better electrical and dynamical performance of the machine. An innovative mathematical model for PMSM under one to four-phase-open circuit faults are established considering the asymmetry of the machine. Combining with time-varying relations in machines’ working conditions, targeted decoupling transformation matrixes of every kind of open-circuit faults are settled by voltage equations under different faults. Modified control strategy with a connection between the neutral point and the inverter’s DC side is presented, which aims at increasing the system redundancy and reducing the amplitude of phase currents. Besides, improved control loops with two layers are put forward as well, with which the PMSM system acquires fewer harmonics in phase current and smoother electromagnetic torque. Simulation and experimental results of open-circuit faults are provided for verification of the theoretical analysis.