Abstract: A 250 MeV superconducting cyclotron for proton therapy has been developed by the China Institute of Atomic Energy (CIAE). The low level RF (LLRF) control system needs to drive two power sources simultaneously to achieve the stability of cavity Dee voltage and frequency and field balance in a precise manner. In order to improve the start-up speed of the RF system, increase the flexibility of the design and meet the special requirements for accelerator output dose and electromagnetic compatibility design in proton therapy applications, a new 250 MeV LLRF control system was designed based on the original design of the traditional LLRF system at the CIAE. The 250 MeV LLRF control system is based on the cPCI bus and adopts a hybrid architecture of FPGA and DSP. The high-speed multiplier and multi-bus structure of the DSP were used to effectively improve the speed of digital control algorithm and enhance the real-time digital processing capability of the system, and the FPGA is used to perform some logic signal processing and communicate with the VxWorks operating system through the cPCI bus, with each of the two controllers performing its own role to improve the operation efficiency of the system. In order to optimize the RF system start-up process and enable closed-loop tuning at extremely low power, the pre-tuning module was added to the hardware design and the low power tuning state was added to the original LLRF control system start-up process to optimize the start-up process. Meanwhile, in order to satisfy the needs of the daily operation of the accelerator RF system and equipment commissioning, the 250 MeV LLRF control system also complements the closed-loop operating in the pulse mode or continuous mode. In addition, in the case of medical superconducting cyclotrons, the electromagnetic compatibility characteristics (EMC) of the medical control systems for medical applications need to be met, so an electromagnetic isolation circuit was added to the circuit design of the 250 MeV LLRF control system to meet EMC requirements. The final results of the system show that the speed of the operation has been effectively increased and that the RF system is able to finally operate stably in adjustable pulse mode during the online commissioning. It has also been demonstrated in electromagnetic isolation tests that the system is not subject to external electromagnetic interference.