In order to reduce the torque ripple and running loss caused by the commutation error in the brushless DC motor (BLDCM) of the magnetically suspended control moment gyroscope (MSCMG), this study proposes a novel method dealing with commutation error in sensorless controlled BLDCM by rapid phase extraction and compensation technique. First, a traditional virtual neutral point circuit consisted of three-phase resistance network and low-pass filter are used to obtain the zero-crossing points of the non-conducting phase back electromotive force without noise interference. Then, an improved phase extraction method is built after analysing the DC-link current. Commutation error is extracted from DC-link current with the improved phase extractor rapidly. Furthermore, the effect of speed offset caused by fluctuation during phase extraction is also analysed and an adaptive commutation error compensation method based on the DC-link current phase extraction is proposed. Finally, simulation and experimental results performed on the high-speed motor of MSCMG verify its effectiveness and rapidity. The main novelties of this study are the direct phase extraction algorithm with natural parameter insensitivity and robustness and the rapid iterative commutation error compensation method based on the extraction algorithm.