Abstract: The Institute of Fluid Physics of China Academy of Engineering Physics independently developed a PET medical cyclotron for medical diagnosis. In order to meet the safe and stable operation of the medical cyclotron, the high frequency system without low level control function was adopted to avoid the danger of direct contact with high voltage. Siemens S7-1500 programmable controller was selected as the front-end controller to complete the accurately scanning of the working frequency about the system, realize the phase and amplitude stability of the high frequency system, and realize the safety interlock and other functions. The results of continuous operation of the system show that the design of the control system meets the requirements of accelerator operation and debugging, and provides strong support for the stable operation of the system.