In this system, the electromagnetic proportional valve is the actuator, and the valve controlled motor is controlled object, and the speed sensor is the feedback element, to send out the orders by industrial computer, to control the motor output speed by controller. According to the principle of the circuit and fluid mechanics, set up the mathematical model of the valve controlled hydraulic motor variable fertilization system. PID parameters tuning of system were performed by Ziegler-Nichols method, get the coefficient of increment algorithm. The step response of P, PI and PID of variable rate fertilization the system were studied by MATLAB/ SIMULINK, results show that: PID algorithm system, the overshoot was small, setting time was short, the number for oscillations was little compared with the P algorithm and PI algorithm, the dynamic performance of the system is excellent. The laboratory experiments results showed that: In the process of system operation, PID algorithm tracking speed was rapid, and steady-state error is smaller. Therefore, the electro-hydraulic proportional variable fertilization system with PID algorithm has good dynamic performance and steady state performance, and can meet the requirements of variable assignment.