This study proposed a high vacuum deoxygenated and water removal glove box control system. Through parameter setting, the system can automatically perform various glove box cleaning operations and quickly reach the micro-oxygen and microwater concentration requirements. In addition, two sets of reaction tanks are built in the system, and the hardware pipeline switching design and monitoring software control are used to provide two sets of reaction tanks to execute the cycling cleaning and cycling regeneration operation procedures synchronously, which can effectively solve the problem of interruption of the experimental process, improve the efficiency of its cleaning operations, and greatly reduce the manpower and material costs of the glove box operation. In addition, the system can automatically record the relevant data during various operations for the analysis of glove box monitoring effectiveness.