For the current aquaculture process of water quality monitoring method has low efficiency, poor real-time, working area is restricted and other shortcomings, designed a water quality monitoring unmanned boat system based on STM32 and Raspberry Pi. The system uses STM32 single chip microcomputer and Raspberry Pi 4B as the controller, combines GPS module and electronic compass to realize the navigation control of the unmanned surface vehicle, uses camera, pH sensor, turbidity sensor and temperature sensor to collect water environment data and water surface image data in real time. Data transmission is realized through 4G communication module. Deploy the upper computer software developed based on the .NET Framework on Alibaba cloud server to implement the functions of issuing commands to unmanned surface vehicle and visualizing the collected data. The results show that the maximum and minimum positional errors between the actual measurement area and the preset area reached by the unmanned water quality monitoring boat for aquaculture are 4.3 meters and 3.4 meters, and the accuracy range meets the actual needs. The average time for water quality measurement is around 7 minutes and 28 seconds, which significantly improves the operational efficiency compared to traditional manual detection methods.The research shows that the system is stable, easy to operate, and can obtain the data of water body in breeding waters in a timely and effective manner, which improves the efficiency of breeding personnel and reduces the cost of breeding, and has certain application prospects.