In this paper, a variable rate fertilization control system for use on granular fertilizer applicator based on DC motors is proposed. It is composed of an embedded terminal and a variable rate controller. By analysis the fertilization theory, the relationship between the parameters affecting the application rate and the position of the gearbox setting lever can be established. The embedded terminal is used to send the control commands through Zigbee wireless network according to the fertilizer prescription map and the real-time GPS information. After receiving the control command, the variable rate controller can adjust the gearbox setting lever in real time automatically by controlling a DC motor precisely in order to change the application rate. The field tests were carried out to test the performance of the control system and the results indicated that the variable rate control system worked well and could meet the requirements of variable rate fertilization.