In order to realize the unattended and autonomous navigation of Wave Glider in the ocean, an autonomous control system is designed, which mainly includes the control circuit part, motor driver part and control algorithm part. System integrates solar energy charging module, wireless communication module, satellite communication module, rudder motor module and data acquisition module etc. In order to improve the intelligence and autonomy, the algorithm of Gaussian earth algorithm, visual tracking algorithm and BP neural network PID control algorithm are used to ensure the navigation accuracy of Wave Glider. To verify the reliability of the system, Wave Glider is tested in the ocean in the aspects of long time running, target points tracking, velocity keeping, and data acquisition. The experiment shows that under normal ocean conditions, Wave Glider can realize the long term autonomous navigation tracking in the ocean, but the speed fluctuates significantly by the current ocean condition; The acquisition of sensor data is normal, stable and reliable, which meets the requirement of long term using in the ocean.