The invention relates to a method for stabilizing and sterilizing wheat germ by the cooperation of microwave and ultraviolet rays, wherein the stabilization and sterilization effects achieved by taking the wheat germ as a raw material and utilizing the cooperative treatment of the microwave and the ultraviolet rays are obviously superior to those of the independent action of the microwave or the independent action of the ultraviolet rays; and compared with the independent microwave stabilization and sterilization, the radiation time needed by achieving the same effect is obviously shortened, and the needed power is reduced. A microwave and ultraviolet combined enzyme inactivation and sterilization device of the invention is arranged in a wheat flour processing workshop, and is connected with a processing production line of a flour mill. A wheat germ processing device mainly comprises six parts such as a microwave and ultraviolet cooperative generation system, a material conveying system, a transmission system, a control system, an air conditioning system, a temperature control system. The method and the device greatly prolong the storage time of the wheat germ, reduce the cost, and are favorable for the industrial development and utilization of the wheat germ.