The mathematical model of the variable rate fertilization control system according to the principles of mechanical and electrical dynamics was set up and the theoretical basis for the system design, parameter selection and performance improvement was provided. The simulation model with direct current servo motor driving variable transmission mechanism was constructed by using Matlab/Simulink dynamic simulation tools. PID parameter tuning of control system was carried out by the critical proportioning method, the simulation curves of system performance was obtained. The simulation results showed that PID control strategy could improve the control system tracking performance and anti-jamming performance, and the test was carried out to verify the system performance.