The invention relates to an intelligent pesticide applying system and a control method of a plant protection unmanned aerial vehicle. The system is provided with a meteorological station used for measuring environment parameters and sending collected data to a ground station. The ground station sends the environment parameters, pesticide applying control parameters and control commands to an onboard pesticide applying controller on the plant protection unmanned aerial vehicle through a wireless data transmission module. Meanwhile, a flight controller measures real-time geographic information parameters and flight parameters of the plant protection unmanned aerial vehicle and sends collected data to the onboard pesticide applying controller in real time. The onboard pesticide applying controller conducts autonomous programmed decisions by combining the flight parameters, the environment parameters, the pesticide applying control parameters and the control commands, a miniature diaphragm pump and two centrifugal atomization disc sprayers are independently controlled, and therefore the pesticide liquid flow, the mist drop diameters and spraying width parameters of the plant protection unmanned aerial vehicle are intelligently controlled. By means of the intelligent pesticide applying system and the control method, it is guaranteed that pesticide in an operation area is quantitative and evenly sprayed in a fully covering mode, the phenomena of repeated spraying and miss-spraying of the pesticide are avoided, the pesticide applying quality is improved, and effective prevention and treatment of farmland pest and disease damage are guaranteed.