In view of the Heilongjiang agricultural reclamation region fertilizer layered problems, a variable rate fertilization control system was developed. It consisted of the vehicle intelligent terminal, the variable rate fertilization controller, four channel speed sensor, four channel hydraulic motor, four channel fertilizer components, GNSS receiver and work status sensor. In order to apply the fertilizer of nitrogen, phosphorus, potassium and micronutrient accurately, a new fertilizer amount strategy with the compound crossover principle was proposed. And then with the PID technology, hydraulic motor control algorithm was designed. When the system started to work, according to the set target values of N, P and K, the actual value of N, P and K would be determined automatically with the corresponding strategy. Subsequently, the hydraulic motor speed would be calculated. Nitrogen fertilizer, phosphate fertilizer, potassium fertilizer and micronutrient fertilizer could be fertilized at one time. In order to verify the effect of the fertilizer amount control algorithm, three experiments were carried out. The results showed that the distributing shaft based on PID control algorithm of response time was less than 0.5s, the system of variable rate fertilization elemental performance error absolute value was no more than 3%. Under the operating condition, it could reduce the use of nitrogen fertilizer obviously and more accurate for N, P and K than that without the algorithm. The control algorithm of the fertilizer amount of the four-factor variable fertilizer application machine completely satisfied the requirements of precise and uniform application of maize fertilization in reclamation area.