Wheat germ (WG) is quite susceptible to deterioration due to the presence of lipase (LA) and lipoxygenase (LOX). Therefore it is indispensable to adopt a stabilization step to decrease the activity of LA and LOX while retaining a maximum level of nutrients. But over-drying can make foodstuffs more susceptible to autoxidation. So a stabilization protocol for inactivating LA and LOX of WG with a temperature- controlled short wave infrared (SIR) radiation system was adopted to retard its rancidity and retain a maximum level of fat-soluble nutrients. Meanwhile, the critical storage water activity (Aw) of WG for inhibiting both hydrolytic and oxidative rancidity was appraised. Results indicate that WG irradiated at 90°C for 20 min acquired the optimal stabilization effect, and its residual LA and LOX activity were 18.02% and 19.21%, respectively. At this condition, the free fatty acids (FFA) content and peroxide value (PV) increment of WG oil at 40°C remained below 5% and 2.24 meq O2/kg for 60 days, respectively. The residual Aw of this WG sample was 0.13, and it is near the Aw corresponding to its monolayer. No significant decrease of fatty acids was observed during SIR processing, while about 96.42% of its original tocopherols still retained in WG treated at 90°C for 20 min.