Abstract— This paper presents a fault-tolerant control strategy for a twelve-phase open-ended Permanent Magnet Synchronous Motor (PMSM) with double stator windings, designed for submarine propulsion systems. Each stator phase comprises two aligned windings positioned symmetrically opposite each other relative to the stator center. To enhance system reliability, modular architecture is adopted for both the motor and its drive system. Each stator winding is independently powered by a dedicated single-phase H-bridge inverter, with individual microcontrollers providing decentralized control. Due to the modular design, each phase operates in its own stationary reference frame. To mitigate torque ripples caused by higher-order harmonics in the back-EMF voltage, a harmonic current injection (HCI) strategy is introduced in the stationery reference frame alongside quasi-proportional resonant (QPR) current controllers. In the event of a phase failure, the proposed fault-tolerant control (FTC) method compensates by dynamically adjusting the amplitude and phase of the remaining healthy phases, thereby minimizing second-order torque ripple. The effectiveness of the proposed approach is verified through comprehensive Simulink simulations under various fault conditions, supplemented by experimental results.