Disclosed is a beam blocking mechanism used in a rotary accelerator proton heavy ion medical apparatus, the beam blocking mechanism comprising a vacuum chamber (8) and a blocking block driving structure, wherein an upper side face of the vacuum chamber (8) is provided with a vacuum chamber cover plate (9); the blocking block driving structure is mounted on the vacuum chamber cover plate (9) and comprises a blocking block (23); an aluminium profile groove (15) is provided on the vacuum chamber cover plate (9), with a gas cylinder (14) being mounted at an upper part of the aluminium profile groove (15) via a gas cylinder holder (16), a linear guide rail (17) being fixed at a central part via a guide rail fixing plate (18) provided in a sliding manner, and a piston rod bushing (13) being mounted on the linear guide rail (17); an upper end of the piston rod bushing (13) is connected in a threaded manner to a piston rod of the gas cylinder (14); and the blocking block (23) is located in the vacuum chamber (8), a lower connecting rod (24) is welded at a lower end of the piston rod bushing (13), and the lower connecting rod (24) is connected in a threaded manner to the blocking block (23).The beam blocking mechanism used in a rotary accelerator proton heavy ion medical apparatus can realise a fast blocking function on an abnormal proton heavy ion beam without affecting the normal operation of other components, thereby guaranteeing the safety of patients and medical personnel.