Abstract: When a two-phase open-circuit fault occurs in a multi-mode high-efficiency permanent magnet fault-tolerant motor, the torque ripple deteriorates, and the remaining phase currents increase sharply. This severely affects the motor’s long-term stable operation and can even cause irreversible damage to the entire motor system. To address two-phase open-circuit faults in this motor, a cooperative control fault-tolerant strategy based on the free distribution of injected currents between the inner stator and outer stator windings is proposed, which can reduce the post-fault current amplitude. Firstly, based on analyzing the novel structure and special flux modulation method of this motor, a mathematical model is established. Four operating modes are then defined according to the current injection methods for the inner and outer stator windings. Subsequently, the fault-tolerant current expressions under different fault conditions are derived using a reduced-order decoupling matrix. By defining the distribution coefficients X and Y for the inner and outer stator currents, an improved fault-tolerant control strategy is obtained, optimized for minimizing the fault-tolerant current. Finally, a motor test platform is built, and the effectiveness and correctness of the proposed fault-tolerant control strategy are verified by experimental tests.