The invention discloses a fault tolerance switching control system and method of a winding segmentation type permanent magnet linear synchronous motor. The fault tolerance switching control system of the winding segmentation type permanent magnet linear synchronous motor comprises a speed setting module, a V curve generation module, a modulation driving module, a maximum thrust tracking module, a power angle detection module, a winding switching fault detection and diagnosis module and a winding switching fault tolerance control module. When a transient state of the system is not stable, the winding switching fault tolerance control module controls the winding segmentation type permanent magnet linear synchronous motor to stop operating and trigger a braking system; and when the transient state of the system is stable, the winding switching fault tolerance control module receives a switching fault signal output by the winding switching fault detection and diagnosis module, and a V fault tolerance control strategy is formulated according to an operation speed of the winding segmentation type permanent magnet linear synchronous motor. With the adoption of the fault tolerance switching control system and method, vibration and stepping-out problems caused by winding switching faults can be effectively solved, and stable operation of the winding segmentation type permanent magnet linear synchronous motor is ensured.