An accelerator-based boron neutron capture therapy (BNCT) experimental facility has been built by Institute of High Energy Physics, Chinese Academy of Sciences. The radio frequency (RF) power source system provides 352.2 MHz pulse power for radio-frequency quadrupole (RFQ) cavity and the beam energy reaches 3.5 MeV through RFQ cavity. The RF power source system includes klystron power source, digital low-level RF (LLRF) control system, and RF transmission system. This paper will introduce the BNCT RF system including physical requirements, system composition, key equipment, installation and commissioning work. At present, the therapy facility operates for animal tests with the target beam power higher than 4.3 kW. The RF power source system runs stably and reliably in the long-term operation.