Wave glider is a new type of marine unmanned autonomous vehicle with characteristics of pollution-free,low energy consumption,long endurance,long voyage,high survivability,etc.,which has gradually been a hot area of research at home and abroad. As an important part of wave glider,the stability and accuracy of control system directly affect the navigation performance,especially the accuracy of navigation and positioning. This paper introduces the design of a wave glider control system based on RT-Thread which is a real-time operating system. This control system has been proved to have good accuracy and reliability through several long-time sea trial.