The invention discloses a permanent magnet fault tolerant motor driving system. The system includes a permanent magnet fault tolerant motor, two sets of three-phase full-bridge driving circuits, two bidirectional thyristors, six fuses, and a separate 270V DC power source; the permanent magnet fault-tolerant motor comprises one set of armature ABC windings and one set of XYZ windings which are independent of each other, are symmetrical with respect to each other and are wound in a manner that each slot is wound with one phase of coils in a three-phase single-layer centralized mode; each set ofthree-phase full-bridge driving circuit is composed of six power switching tubes; the two sets of three-phase full-bridge driving circuits respectively control the ABC windings and XYZ windings of the permanent magnet fault-tolerant motor; when the system fails, a corresponding bidirectional thyristor is turned on, so that a half-bridge power conversion circuit with a neutral point is formed, andtherefore, the control of the fault-tolerant operation of the system is realized. The permanent magnet fault tolerant motor driving system of the invention has the advantages of magnetic isolation, physical isolation, thermal isolation, small cogging torque ripple, suppression of short-circuit current, and high fault tolerance, and can realize fault-tolerant operation under a condition that different electrical faults occur alone or simultaneously.