Underwater glider is a new type of long-range underwater robot, which can sail for several months with its efficient driving mode. Therefore, compared with other autonomous underwater vehicles, the reliability of glider control system is particularly important. According to the long-range requirement of underwater glider and the architecture of its distributed control system, a master-slave emergency control technology is designed. By means of CPU mutual monitoring and establishing common storage area, the non reset hot switch is realized under the abnormal condition of the controller, which ensures the normal operation of the important moving parts of the glider. The test results show that the master-slave interactive control mode can greatly reduce the impact of the main CPU outage on the autonomous operation of the glider, and increase the safety performance of the underwater glider.