For the multiple-canned-motor system used for vacuum pumps, fault shutdown may occur under different conditions such as starting, sudden random disturbance, sudden cyclic load, single motor failure, and multi-motor asynchronous failure. Aiming at this problem, a mode switching and position compensation deviation coupling synchronous control system is designed. The position compensator is innovatively introduced into the speed compensator and the deviation coupling control mode is switched to master-slave control at the moment of fault shutdown. The proposed control system is compared with the traditional virtual motor synchronous control system. The results show that for single motor failure and two-motor asynchronous failure, after mode switching and position compensation, the position errors of the proposed control system are 4.6° and 4°, respectively, which are smaller than the position error tolerance value of 5°. In comparison, the position errors of the traditional virtual motor control system are 15° and 20°, respectively.