To improve the resource utilization, reduce the pollution generation, and increase the economic benefits of enterprises, a cleaner process to produce cassava starch was proposed based on potato starch processing, and it was applied to the transformation of a traditional cassava starch processing factory in the Guangxi Province in China. The transformation involves the implementation of several new techniques/facilities, including a rasper, horizontal centrifuge, and hydrocyclone. Based on the transformation, typical cassava starch factories in Guangxi were evaluated. The results show that, through the application of a series of cleaner techniques/facilities, the starch recovery rate increased to 84.5%. The water consumption, wastewater generation, and chemical oxygen demand generation decreased by 53.8%, 49.0%, and 20.7%, respectively. Based on the cleaner process, the wastewater can be treated to meet the national discharge standard by using common wastewater treatment technology.