According to the rapid responses and high precision control requirements of grain counter production process, the control system was designed, which was based on the DSP of TMS320F2812, combined with liner array CCD, ARM9 miniature controller and other hardware. The construction, function, working principle, and working flow of the grain counter control system was introduced. Among the subsystems, the subsystem of detection and counting pill and hyaline capsule is the difficult point, which is also the foundation of ensuring the control precision. The schematic diagram, working flow, and operation result chart of the grain counter, the working time sequence chart of CCD, and algorithm of computing the channel priority based on self-organizing neural network were given. The control system has high counting precision, fast working speed and stable operation