Multi-phase permanent magnet fault-tolerant motors are often used in aviation, transportation and military fields which require high reliability of drive systems. Open circuit fault is a common electrical fault in motor drive system. Aiming at the problems that the existing fault diagnosis methods need to identify the open circuit fault of switch tube and winding with multiple sets of variables, and the change of motor running state is easy to lead to the misdiagnosis of threshold value judgment, this paper proposes a new phase voltage average value algorithm, which combines the motor drive system with the current mode flux observer. and switches the diagnosis variables from fault complex identification to a group of variables identification, and from threshold range diagnosis to a group of positive and negative variables the different open circuit faults of switching tube and winding can be distinguished by the diagnostic results. The experimental platform for fault diagnosis of six-phase permanent magnet fault-tolerant motor is built, and the experimental results verify the effectiveness and superiority of the proposed algorithm.