To improve the utilization rate of maize seed fertilizer, this study aimed to propose a precise co-sowing control system for the real-time control of the relative position of seed fertilizer during the co-sowing operation. According to the operating speed of the machine, the longitudinal distance between the seed feeder and the outer groove wheel, the height of the seed and fertilizer falling, and the relative position of the seed and fertilizer falling into the soil, the calculation method for the seed and fertilizer falling into the soil was obtained, the precise co-seeding model of the seed fertilizer was constructed, the control algorithm of the precise co-seeding of the seed fertilizer was designed, and the hardware system and software system were designed. Based on the hardware structure and working principle of the motor drive seeding and fertilization control system, a functional circuit based on the STM32F103ZET6 single-chip microcomputer (Zhengdianyuanzi (Guangzhou) Technology Co., Ltd., Guangzhou, China) was built. When the system is working, the satellite speed measurement module collects the operating speed of the machine, the encoder feeds back the motor speed in real time, a Hall sensor detects the time interval between fertilizer and seed discharge at the point of discharge, and the PID algorithm is applied to make the speed regulation system regulate the motor speed and position and adjust the speed and position of the seed discharge tray and fertilizer on the outer slot wheel in real time. The relative position of seed and fertilizer in the soil can be controlled accurately in the process of sowing fertilizer. The test results showed that when the feed speed was 2, 3, and 4 km·h−1, and the grain spacing was 20, 25, and 30 cm, respectively, the seed fertilizer alignment was better and met the requirements of precise sowing, improving fertilizer utilization rate.