Aim to the problems of complicated adjustment of PID parameter, time-consuming and strongly empirical in variable rate fertilization system, genetic algorithm PID (GA-PID) tuning method was proposed to implement flexible parameter adjustment. By using Matlab/Simulink simulation, the square wave response of traditional PID and GA-PID system were compared. The results showed that GA-PID control strategy was superior to the conventional PID in response speed, overshoots, and setting time. System steady performance experiment was carried out at variable rate fertilization test bench. The results showed that GA-PID control algorithm of variable rate fertilization system was very accurate, the static error was small, and speed range linearity as good. GA-PID retrenched the process of parameter tuning and optimized the parameter tuning results.