The aquatic plants comb-collect boat has gradually become an important equipment for the management of aquatic plants in river crab breeding ponds. In order to realize the automation of the aquatic plants comb-collect boat, an automatic navigation control system for the boat with a fan as the driving device was designed and developed. Firstly, a set of the aquatic plants comb-collect boat software and hardware control system was designed； Then, the dynamic model of the aquatic plants comb-collect boat was established and verified by experiments； Then, the motion control and path tracking of the aquatic plants comb-collect boat were realized by using the heading estimation PID control method and the LOS circle of sight method； Finally, the speed test, path tracking and waterweed harvesting experiments were carried out in the farm. The results show that the maximum speed of the aquatic plants comb-collect boat can reach 1.14m/s, the PID heading control method and the LOS circle of sight method can accurately realize the path point tracking of the aquatic plants comb-collect boat. In good weather conditions, the average error of path tracking is less than 0.96 m. compared with the manual method, the cleaning weight per unit time is increased by 94.3%, which effectively reduces the labor intensity of harvesting aquatic plants and improves the automation level of aquatic plant management in crab ponds.