Aiming at the problems of high failure rate, difficult maintenance, poor flexibility, and dangerous manual operation of the traditional stand-alone control of the proton beam irradiation thorium target loading and unloading system under the operating environment of low radiation, large scale, and high complexity, a control method of digital twin proton beam irradiation thorium target loading and unloading system based on the redundancy of Programmable Logic Controller (PLC) is proposed. Firstly, the method adopts a multifactor coordinated control strategy such as CPU redundancy, I/O redundancy, and power supply redundancy, and enables the control system to run uninterruptedly by constructing a hardware hot-standby redundancy system and organizing, programming, and simulating a software redundancy system. Secondly, based on the architecture of “NX MCD+PLC SIM+OPC”, the control system of digital twin virtual-reality interaction is designed, and the twin model of target loading/unloading system is constructed in the virtual space for the data information in the physical space, so as to realize the unattended and continuous monitoring in the radiation environment. Finally, experiments and reliability analysis, prove that the proposed method improves the stability of this control system to 99%, which provides a new idea for the control of operating system under irradiation environment.