The traditional air-assisted side-deep fertilization device has some problems, such as inaccurate parameters of control system and poor precision of variable fertilization. It seriously affects the application and popularization of the device. Aiming at the above problems, this paper want to realize the precise control of air-assisted side-deep fertilization device. This paper constructs an electronically controlled fertilization system based on PID controller. The system model is built in MATLAB, and the transfer function of control system is deduced too. In order to improve the accuracy of control system parameters, the system parameters were optimized based on particle swarm optimization algorithm and control system tuner toolbox. The optimized system parameters of Kp, Ki, and Kd were set 3.05, 10 and 0.32, respectively. The experimental platform of variable fertilization was built according to the system parameters, and the mathematical model of variable fertilization was calibrated. The mathematical model’s R2 was 0.99. The optimized system parameters were imported into the controller, and the controller converted specified fertilizer quality to rotary speed of stepping motor. The driver ordered stepping motor to drive fertilizer discharge shaft at the set rotary speed by the controller. The experimental results showed that the maximum deviation of fertilization rate was 10.76g, which could better meet the requirements of precision fertilization. This research can improve the evenness and accuracy of the application of electric control fertilization.