As one of the core contents of USV development, the autonomous navigation control system of USV is the precondition for USV to perform various missions. The excellent navigation control performance is conducive to the smooth realization of USV operation tasks. This paper mainly studies the design and typical application of USV navigation control system. Firstly, the architecture of USV intelligent control system is designed based on the theory of brain basic function joint area; Then, under this architecture, the software and hardware design and implementation of USV navigation control system are deeply studied with the "Sea sturgeon" series USV as the research object. Finally, the typical application scenarios of unmanned craft are discussed, which can provide a reference for the research of autonomous navigation control system of USV and the construction of unmanned craft equipment in China at this stage.