In order to improve the positioning accuracy of the stepper motor,the design of steper motor closed-loop control system based on AT89S52 is proposed in this paper.The AT89S52 microntroller is used to receive instructions from PC by serial port and produce corresponding control signal.Therough controlling the stelpper motor by RD-053MS stepper motor drive,the angle encoder and IK220 counter card are used to obtain the rotation angle and the target rotation angle,and sends motion instructions to the AT89S52 microcontroller until the instructions meet precision requirement.The experiment shows that the positioning accuracy of the system can be controlled in less than 20 second of arc,and can be applied into many CNC system.