The invention discloses a wave glider fault-tolerant control system and method with an emergency function, and belongs to the field of wave glider control. The wave glider fault-tolerant control system comprises a main control system, an emergency control system, a communication system, a sensor system and a steering engine; the main control system comprises a main control computer; the emergencycontrol system includes a monitoring computer and a first relay; the communication system includes an iridium module, an iridium antenna, a GPS antenna, and an AIS communication module; the main control system and the sensor system communicate with each other through a serial port; the main control system and the monitoring computer communicate with each other through a serial port; the monitoringcomputer and the main control system are connected through a first relay; the emergency control system and the steering engine communicate with each other through a serial port; the emergency controlsystem and the iridium module communicate with each other through a serial port; the emergency control system and the AIS communication module are connected through a second relay; the iridium modulehas a GPS interface and an iridium interface; the iridium antenna is connected to the iridium module through the iridium interface; and the GPS antenna is connected to the iridium module through theGPS interface. The wave glider fault-tolerant control system has high running stability, strong fault tolerance and self-repairing ability, and significantly reduces the risk of missing and losing thewave glider.