China Institute of Atomic Energy (CIAE) is constructing a high current cyclotron-based boron neutron capture therapy (BNCT) system. The designed proton beam intensity of this cyclotron is 1 mA. The RF system of the cyclotron consists of two separate cavities, two 20-kW amplifiers, a 300-W amplifier for the buncher, and one low-level radio frequency (LLRF) system. The LLRF system controls the amplitudes and phases of the two independent cavities and the buncher. The previous analog–digital hybrid LLRF system in CIAE was designed for low beam loading applications. As during the beam commissioning and machine operation, the RF system requires a more powerful, flexible, and reliable real-time LLRF system, the LLRF group decides to design a new LLRF system for this application. At TRIUMF, a digital LLRF system was developed for the prebuncher of the ARIEL project. This state-of-the-art design is extended and utilized for the BNCT LLRF system. In which, the amplitude and phase of the two separate Dees, as well as the buncher for beam injection, will be regulated by a single field-programmable gate array (FPGA). For such a demanding control task, the design shows a promising future, both from real-time response and flexibility points of view. The design ideas, technology features, system structure, hardware and software development, and the desktop test will be presented.