Microwave processing technology and equipment were developed to solve the problem of wheat germ’s easily acidification and deterioration, aiming at improving the storage stability of wheat germ and better prepare for its further processing. With this developed equipment, microwaves of different power and processing time were selected to test their respective influence on the wheat germ stabilization. The result showed that processed with microwave of 2.8kW for 4 minutes, wheat germ relative lipase activity is 17.63％, peroxide value is 3.81mmol/kg, acid value is 14.65mg/g，VE loss is 5.29％，NSI is 51.10％，moisture content is 3.72%, and no distinct change in its fatty acid composition and relative content. Furthermore, the equipment developed was tested to be collocated with wheat flour product line with the daily capacity of producing 300t. This equipment effectively passivates lipase in wheat germ, preserves various nutrition, and lengthens quality guaranteed time at the cost of lower power.