In flywheel energy storage system (FESS), multi-phase motor can be used to drive the flywheel for its high power density and fault-tolerance performance. Aiming at the two-phase fault in different sets of three-phase windings in twelve-phase permanent magnetic synchronous motor (PMSM), afault-tolerant control strategy based on motor model reconstruction is proposed in this paper. The set of three-phase windings that has phase failure is controlled as single-phase motor. Therefore, the twelve-phase PMSM is treated as an integration of two three-phase motors and two single-phase motors. The proposed strategy maintains stable torque and power during fault-tolerant operation. Theoretical analysis and simulation are carried out in this paper, and the results demonstrate that the proposed strategy has good effectiveness on two-phase faults in two sets of wingdings, no matter the two phases are orthogonal or not.