With the aim to simplify the electrical component structure of the present variable rate fertilizer applicator system, a kind of variable rate fertilizer applicator control system was developed. It is based on low voltage DC motor. The working voltage of this system is not higher than 12V DC, which can be supplied by the tractor’s storage battery directly. With the encoder measuring the motor speed, it could response the running state of the motor in real time. A kind of control model based on PID algorithm was built. With this model, the influence of load variation on the motor speed could reduce. As a result, the control accuracy of this system could be improved. Field experiment has been conducted using this system. Experiment showed that when the travel speed was 3.60km/h, the maximum fertilizer rate could be 850 kg / hm2. When the fertilizer rate was 200 ~ 600 kg/ hm2, the mean error of this system was 1.71% while the maximum error was 2.56%.