Abstract The performance, efficiency, and stability of semiconductor materials are directly influenced by the quality of wafer cleaning, which is a crucial step in the production of integrated circuits and photovoltaic cells. For this reason, the final product’s quality greatly depends on the cleaning effect’s quality. Approximately half of the issues and malfunctions in large-scale integrated circuits are related to inadequate cleanliness of the silicon material, a result of the shortcomings of current wafer cleaning technology. Wafer cleaning process optimization is therefore crucial. The control system is designed based on the structural features and process flow of the chemical liquid spray wafer cassette cleaning machine. Siemens S7-1200 PLC is used as the control core of the control scheme, which is built by examining the control principles of each cleaning machine module and choosing and designing the hardware component of the control system. The wafer cleaning process is fully automated thanks to the design of the upper computer monitoring interface, which also includes a touch screen for online debugging. This significantly raises the production efficiency of the wafer-cleaning machine.