Application of protection materials is a crucial component in the high productivity of agriculture. Motivated by the needs of aerial precision application, in this paper we present a pulse width modulation (PWM) based precision spraying system for unmanned helicopter. The system is composed of the tank, pipelines, pump, nozzles and the automatic control unit. The system can spray with a constant rate automatically when the speed of the UAV fluctuates between 1 m/s to 8 m/s. The application rate can also be controlled by remote control terminal the automatic control unit is the core of the system which is composed of double-channel PWM controller, wireless communication module, GPS module and MCU. MCU obtains the helicopter flying speed real time and changes the output rate by moderating the flow of the pump and On-off time of the nozzle. PWM controller designed basing on the embedded PWM generator of ATmega128A and dual full-bridge driver chip L298. By the theory analysis and experiments in laboratory, the relationship model of output rate with helicopter flying speed and pump output rate with on-off time ratio of the nozzle were built. The optimal operating parameters of the system were obtained. If the pipeline pressure keeps constant, the output rate could be adjusted from 0.19L/min to 0.78L/min. If the PWM control method cooperates with regulation of  pump work voltage, the output rate could adjusted from 0.10L/min to 1.28L/min. Tests for system performance are carried out and the results show that the controller has promise as a higher precision technique for spray applications, which will improve efficiency of pesticide application. The development of the UAV spraying controller has a great potential to enhance pest management over small crop plots or spots within a large crop field to realize highly accurate site‐specific application. It is also very promising for vector control in the areas that are not easily accessible by personnel or equipment.