Medical cyclotron is widely used in the fields of national defense basic science research, isotope production, diagnosis and treatment. High stability and security of medical cyclotron system are required in these situations. Based on these application requirements, this paper outlines the composition of the control system, briefly introduces the role of each subsystem, and finally the system integration with RX3i programmable controller as the front-end controller, the control strategy of low-level control of high frequency system and the security interlock of each system under different working modes are elaborated in detail. The results of continuous operation show that the control system ensures the stable operation of the whole system and meets the requirements of accelerator operation and debugging.