China’s flour industry has gradually transformed from small and scattered to intensive and large-scale production, the types and amount of hazardous waste generated during the process have also increased. However, the foundation of hazardous waste storage management in flour industry is weak, and it is urgent to standardize and strengthen the selection, construction and operation management of hazardous waste storage sites. Through the analysis of the characteristics of hazardous waste in flour industry, the types of storage location are reasonably selected. The construction elements are decomposed and refined from five dimensions: building requirements, packaging containers, electrical safety, material allocation, and visual identification. The safety and environmental measures are proposed, and the construction model for hazardous waste storage sites in flour processing industry has been constructed. At the same time, in order to address the issue of non-standard management, a full process compliance management approach for hazardous waste storage has been proposed from three aspects: inbound management, storage management, and outbound management. This paper will provide reference for promoting and guiding the flour industry to construct and manage hazardous waste storage sites standardizedly and systematically.