Due to the different soil nutrients in different depths of orchard, and the ability of fruit tree roots to absorb fertilizer is different, the layered variable deep application of organic fertilizer can solve the problems of uneven distribution of nutrients and low utilization rate of fertilizer in traditional fertilization. In view of the electro-hydraulic control of layered variable rate fertilizer discharge, a fertilizer discharge control system was designed, which can calculate the theoretical speed of hydraulic motor in real time according to the theoretical fertilizer amount of each layer set by the user and the forward speed of the unit. PID algorithm was used to control the opening of the proportional flow valve, and the motor speed was adjusted to drive the screw conveyor to discharge fertilizer, so as to realize the layered variable rate fertilizer discharge. PID algorithm usually needed to adjust the parameters such as proportion, integral, differential coefficient and sampling time to obtain better control performance. Matlab/Simulink is a powerful simulation software, which can establish the control system model and carry out simulation. It can quickly and conveniently adjust PID parameters. But it is necessary to establish the mathematical model of the controlled object. It is difficult to establish an accurate mathematical model for the valve controlled motor speed control system because of its nonlinearity, time-varying and hysteresis. AMESim is a multi-disciplinary complex system modeling and simulation platform, especially suitable for hydraulic system simulation and analysis. The hydraulic system model was built in AMESim, the control model was built in Matlab/Simulink, and the joint simulation results were more accurate and reliable. The hydraulic system mainly included gear pump, relief valve, differential pressure reducing valve, proportional throttle valve and hydraulic motor. According to the sample of hydraulic components, the hydraulic system model was completed in AMESim, the parameters of each component was set, the rotating load was set according to the actual working environment, the speed sensor and coupling interface was added. The PID control simulation model was established in Matlab/Simulink, and the parameters were adjusted through joint simulation. When the values of proportional, integral and differential coefficients were 0.005, 0.05 and 0, respectively, and the sampling time was 0.5s, the control performance was the best. The adjusted algorithm was used in the bench test of speed regulation performance and fertilizer discharge performance. The regulation performance test results showed that the speed regulation performance was good, the maximum overshoot was 14r/min and the maximum time to reach the stable speed was 6s. The simulation results were accurate and reliable, AMESim-Matlab/Simulink joint simulation can quickly and conveniently research the layered variable rate fertilizer control algorithm, and adjust algorithm parameters. The fertilizer discharge performance test results showed that the accuracy and uniformity of fertilizer discharge can meet the requirements, the maximum relative error of fertilizer discharge was 6.20%, the maximum coefficient of variation was 8.69%. The control system had better control performance, and it can provide technical support for layered variable rate deep application of organic fertilizer in orchard.