In the wake of development of China’s agricultural aviation technology, the application of microplant protection unmanned aerial vehicles (UAVs) in the domain of crop pest and diseases management is becoming more and more extensive. There is no doubt that the UAVs have some significant advantages comparing with the traditional spraying methods because of its features of flexibility, environmental adaptability and high operational efficiency, particularly when working under complex scenarios that are inaccessible for conventional plant protection equipment. However, in practical applications, there are still some notable issues such as unsatisfactory application quality, low automation, and high safety risks which are limiting UAV’s working performance. Precision spraying technology and UAV autonomous control technology are the key factors in terms of ensuring the spraying quality, improving working efficiency and safeguarding flight safety. For the sake of endowing the UAV with some extent of autonomous flight capability, a multilayer control system was introduced, which consisted of a companion computer and an opensource flight controller that can communicate with each other via ROS and MAVROS. Meanwhile, an integrated method of external sensors (RTK-GPS and LiDAR sensor) and flight controller onboard sensors was proposed. This method can significantly improve the spatial position and control accuracy of the plant protection UAV. In order to further enhance the UAV’s autonomous flight ability, the task control system was designed and proposed, which enabled UAV autonomously flight between multiple task points with the horizontal and vertical location error of 0.145m and 0.053m, respectively. The research result effectively improved the plant protection UAV’s position accuracy and selfoperating performance, and provided some reference for the future development of precision spraying technology.