The invention discloses a safe interlocking protection system of a proton therapy accelerator. Safety-type PLC is adopted as a data processing and executing component, the protection system is connected with a water cooling system, a vacuum system, a superconducting magnet system, an ion source system and an RF system, wherein the water cooling system is used for using flowing cooling water to take away heat generated by the operation of the accelerator, the vacuum system is used for providing a vacuum environment for the operation of the accelerator, the superconducting magnet system is usedfor providing a stable magnetic field environment for the operation of the accelerator, the ion source system is used for guiding proton beams from hydrogen molecule ionization, the RF system is usedfor providing an accelerating electric field for particles and maintaining the electric field stability in the accelerator through feedback control, fault and state signals of the sub system of the accelerator are collected by a safe interlocking system of the accelerator, and an interlocking signal of the sub systems of the accelerator is distributed by the safe interlocking system of the accelerator. By means of the system, the sub systems of the accelerator can be controlled to ensure the safety of the adjacent sub systems, and the damage to equipment is reduced to the maximum extent.