In order to improve the torque-output precision of the magnetically suspended reaction flywheel, compensation methods were proposed respectively to attenuate the undesirable torque ripple caused by nonideal back electromotive force waveform and commutation in classical control of brushless direct current motor. The real-time back electromotive force was estimated according to the rotor position and speed in order to obtain the reference current, the pulse width modulation duty cycle was calculated in the torque controller to compensate the torque ripple caused by the nonideal back electromotive force. The theoretical derivation was analyzed, methods of modulation of the non-commutation phase during low-speed range and modulation of the switching-out phase during high-speed range were presented on the basis of the characteristics respectively. Also, a calculation method of the commutation time was given. The experimental results show that the proposed methods can achieve an effective compensation.