In order to improve the situation of excessive use of fertilizer and low utilization of fertilizer, a variable rate fertilization control system based on matching fertilizer line and seed line was designed. The system was composed of four modules, including electric control module, hydraulic module, mechanical module and vehicle terminal. Firstly, automatic navigation system installed on the tractor was used for navigation fertilization and navigation sowing. According to the width of the mechanism and the location of the fertilizer (seed) tube, the navigation line was shifted to match seed fertilizer line，accurately. Subsequently, according to the target value, the actual rotation speed would be determined automatically by the corresponding strategy. The experiment results showed that the field matching error was within 6cm and more than 90% of the data points were within 3cm. The results of field experiment showed that the errors of the fertilizer value were less than 2.70% and the variation coefficient was less than 005 at the shallow layer. The errors of the fertilizer value were less than 7.95% and the variation coefficient was less than 0.08 at the deep layer. In the field experiment, traditional fertilizer application zone and reduction of 12% zone were set. The corresponding yield were 3900kg/hm2 and 3945kg/hm2 in 2018. Compared with the traditional fertilizer application, the yield of reduction of 12% zone had no significant difference. The variable rate fertilization control system based on matching fertilizer line and seed line provided a new method to reduce the excessive uses of fertilizer for wheat growth.