The fat-related enzymes of whole wheat flour cause the increase in fatty acid value, the tallowiness of whole wheat flour and the higher microbial count. This seriously affects the shelf life of whole wheat flour and restricts the circulation and sales of whole wheat flour. In this study, the key physical and chemical indicators, as well as microbial count of several commercially available whole wheat flours are analyzed and compared. The results show that after 3 months of storage, the fatty acid values of the whole wheat flour are close to or slightly higher than the industry standard requirements. The bran prepared in laboratory was treated with atmospheric steam at different times. The results showed that after 10 minutes of steaming treatment, the total plate count in the bran decreased from 2.2×105 CFU/g to 1.4×102 CFU/g, and the spores count decreased from 1.2 ×103 CFU/g to 1.1×102 CFU/g. After 20 minutes of atmospheric steaming treatment, the total plate count and spores decreased to less than 100 CFU/g. Atmospheric steaming treatment for 10 minutes can inactivate the bran lipase and lipoxygenase by 90% and 80%, respectively. The whole wheat flour was prepared by adding bran that has been steamed for 10 minutes back to the flour. Based on the results of whole wheat flour shelf life test, we therefore conclude that the shelf life of whole wheat flour is at least 16~17 months.