In order to study the impact of microwave radiation on wheat germ (WG) quality, a continuous microwave radiation system was constructed. Scanning electron microscopy and micro viscometer were used to detect the influence of microwave radiation on microstructure and starch pasting characteristics of WG. The results showed that the continuous microwave radiation system had a good stabilization effect on WG. The majority starch granules in microwave-treated WG were still intact observed by SEM, accompanied by a clear outline. However, with the microwave radiation intensity increased, the original spatial structure changed among starch granule, oil and protein. The gelatinization temperature of microwave treated WG rose to a range of 59.3～65.4℃. Depending on their extent of pre-gelatinization, different WG samples gave significantly different peak viscosity (349～466 BU) and break down values (69～87 BU). Compared with that of raw WG samples, the fatty acids composition and tocopherol content of WG treated by microwave did not change significantly. The above results showed that microwave radiation did have some effect on WG quality, but less than traditional heating methods. Microwave stabilization should have a good prospect for industrial application.