This study aimed to investigate the effect of superheated steam treatment (SST) on lipid stability of whole wheat flour (WWF) during storage. After SST, the lipase and peroxidase of WWF were inactivated, and lipoxygenase activity was lower than 5% of its initial value. The total tocopherols decreased slightly in all SST groups, especially it only decreased by 1.1% at 190 °C for 5 s. Furthermore, the increase of fatty acid value in the control group was over 100-fold than that of the SST groups during storage. The unsaturated fatty acids and total tocopherols in WWF decreased gradually, but the decrease was alleviated by SST at 190 °C for 5 s. After storage, the relative content of hexanal and 2-pentylfuran in the SST groups were 4 and 0.3-fold than those in the control group, respectively. Thus, SST may be a potential approach to stabilise the quality of WWF.