In order to meet the requirements of the periodic cutting and cleaning of aquatic plants in river crab aquaculture, a small and medium sized intelligent automatic aquatic plant cleaning ship based on ARM was designed. Then the mechanical structure and working principle of the integration of harvest were introduced, and the ship’s main structure characteristics were also put forward, such as the paddle propeller without a rudder, rotary cutting device, cut deep automatic adjustment regulator and so on. The closed loop control system of GPS navigation for the ship was designed with PD and PI control technology of intelligent mobile robot, and high precision GPS navigation control technology. The experiment results showed that the control precision of linear track could be controlled precisely within the scope of ±30 cm. On the basis of meet harvest requirement, the control system can avoid the repeat cutting or miss cutting caused by yaw effectively.