A control system for variable rate fertilizer machinery with a single chip ‘AT89C52' was designed and built. It received the positioning signal from GPS and identifies the operation cell where fertilizer machinery locateed in. By reading the signal of sensor of fertilizer machinery and the application rate of fertilizer of the operation cell stored in IC card, the system controled the rotate velocity of fertilizer feed. Then the fertilizer mechanism could work automatically in real time. The experiment showed that the control system could synthetically process the signals of GPS, GIS, the sensor and the decision data. When the application rate of fertilizer was more than 200 kg/hm² and the fertilizer machinery velocity was between 4.5 km/h and 5.5 km/h, the control system could make the fertilizer feed run at 33～91 r/min. The average error of the application rate of fertilizer was less than 4.22%.