Abstract In this paper the plant protection UAV control system based on Pixhawk flight controller has been proposed, which the system consists of two subsystems: flight control system and spray system. Based on PX4 firmware has been adopted to achieve the Pixhawk flight control. Communication protocol has been analyzed in detail and communication control between flight controller and the spray controller by serial port has been realized. The software part has been designed the remote control decode task and the spray task in the flight control system and spray task in the spray system. At last taking the plant protection UAV as the object, the communication between the flight control system and the spray system have been realized to completed spray function successfully.