A real-time control system of the automatic variable rate fertilizer applicator was presented. The control system takes PLC as the mainframe, and integrates with the optical sensor and automatic control equipment. The quantity of fertilizer was adjusted with the tractor speed and the crop spectrum data by real-time measuring. The technology of non-destructive test and the fuzzy control algorithm was adopted in the system. According to the speed of the tractor and the real-time value of NDVI (normalized difference vegetative index) from NDVI equipment, the real time variable rate fertilizer was realized via opening or closing the electromagnetic valves of the system.