In order to solve the problems of difficult manual handling, high technical requirement, low efficiency and high cost during the exchange of the cell medium before cell freezing, a design of automatic control system based on STM32 and μC/OS-Ⅱ is proposed. In the system, STM32 is used as main controller to complete the generation of S-shaped acceleration and deceleration pulses for the stepper motor, acquisition of displacement data and analog-to-digital conversion, communication with the host computer, etc. Embedded real-time operation system μC/OS-Ⅱ is applied in the control system, which can realize the multi-tasks running, simplify programming and is easy to extend. Test results show that the system is stable, feasible, and has greatly shortened the test time, which reaches the preliminary requirements of the design.