Inoculation separation is a widely used operation in medicine, whose use of manual operation is timeconsuming and easy to infect the medical staff. In order to achieve high efficiency, accuracy and automation, a type of automatic control system with ARM series STM32F407 chip as the core was designed, which was equipped with corresponding sensors and actuators. This system could control the action of each executing part in the medical rowing machine, and exchange data with external scanners, RFID card reader, touch screen and the PC to implement such functions as sample collection, germ culture, collection and storage of experimental data and fee deduction authorization. The machine could take the place of traditional manual operation, truly realize aseptic operation, reduce the probability of virus infection among medical staff, and fill the gap of current domestic technology. The result of the testing has been accepted by hospitals, and now the machine is getting into small scale production.