Abstract: China Institute of Atomic Energy has built a high intensity proton cyclotron with extracted beam energy of 100 MeV and designed current of 200 μA. In order to reduce the beam loss during particle acceleration, the working vacuum in the particle acceleration chamber is required to be 6.7×10^-6 Pa. Because it’s compact structure, the pump of vacuum system provided by the accelerator is very limited. In order to increase the overall pumping capacity of the system, the main vacuum system was designed as a plug-in cryopanel combined with an external cryogenic pump. The designed vacuum system was installed in 100 MeV high intensity proton cyclotron. It provides a favorable guarantee for beam adjustment and normal beam supply of the accelerator.