In order to successfully realize the task of unmanned surface vehicle (USV), the design and typical application of USV navigation control system are studied. The architecture of USV intelligent control system is designed based on the theory of basic functional areas of the brain. Under this architecture, the software and hardware design of USV navigation control system is studied, and the typical application scenarios of USV are discussed, taking the “sea sturgeon” series USV as the research object. The results show that the research can provide a reference for the research of autonomous navigation control system and the equipment construction of unmanned boat in our country at present.