In some industrial applications, the brushless DC motor needs to maintain its operating condition in the case of the rotor eccentricity, and the traditional control strategy was difficult to achieve fault tolerance with it. Aiming at this problem, a fault tolerant control strategy for the brushless DC motor with rotor eccentricity was presented. First of all, in the conventional brushless DC motor control method, stator current commands were similar in shape and delayed by corresponding phase differences in each phase, without considering the change of the back electromotive force and the c phase inductance caused by the rotor eccentricity, so the unknown torque ripples would happen. Therefore, a novel control strategy based on traditional control strategy based on the online estimation of the phase inductance and back electromotive force value, thereby setting the stator current reference controller consists of eccentric fault. Then the motor could reduce the torque pulsation, and had the fault tolerant ability. The contrast experiments had been taken to verify that the proposed method at the last.