Grain reserve is the important material basis for food safety, and the grain storage management is core business for grain reserve security. In this paper, the whole process of grain storage management was classified into preparation, input, storage and output such 4 process and 23 steps, which can match the problems occurring in each process with 6 essential factors including human, machine, material, method, environment and measurement and 15 subdivision factors based on the matrix graph method. Six key control points, such as warehouse tidiness, personnel technical ability, grain origin investigation in the preparation, technology and equipment, operation rules and regulations in the storage, and quality control of sample determination in the warehouse link, were identified through by the Pareto chart. This study put forward some countermeasures and suggestions to ensure the quality of grain reserves and improve the standardization of storage management in the new period based on the key control points.