Appropriate amount of fertilization in an accurate position is the basic requirement for meeting the precise fertilization operation in the field. The domestically used groundwheeldriven fertilizer applicator can not be controlled in real time to meet the requirements of fertilization accuracy. The outergroove wheel fertilizer has a simple structure to be controlled by a motor easily. In order to realize the positioning and fertilization operation based on the root position of the corn seedling stage, a position fertilization control system was designed based on a motor drive, which mainly included the master computer, the slave computer processor, the motor and the driver. The problem of fertilization lag was widespread in fertilization research, which was effectively solved. The factors causing the delay time were analyzed and the lag model of the fertilization position was established, the stability of the control system was improved and the error was reduced. A threshold control algorithm was proposed for placing the lag distance as the advance amount into the control system. The stability and accuracy of the control system were verified by a test platform. The test results show that the control system can control the speed of the fertilizing motor in the range of 50～201r/min stably, and complete the position fertilization with an average response time of 0.8s. The results of this study can reduce the delay of fertilization and improve the accuracy of fertilization positioning.