Abstract: It is necessary to measure beam parameters with beam diagnostics detectors for HIMM(Heavy Ion Medical Machine), most of which are interceptive detectors that will be inserted into the center of the beam pipeline while measuring the beam parameters and be pulled out when the measurement is finished. Furthermore, some of the detectors need to be controlled harmonically. In this paper, the architecture of the motion control system is designed and implemented based on the EtherCAT protocol. The client-server software system based on OPC UA protocol is developed and tested with beam. The motion control system of all beam diagnostics detectors has passed the verification of the CFDA(China-Food and Drug Administration) and been running since 2017 with beam. The results show that the system is of high stability and transplantability characters, the control accuracy and control mode can fully meet the application requirements.