The invention relates to the field of grain processing, in particular to a conditioning method capable of reducing the microorganism content in wheat. The method comprises the steps of cleaning unprocessed grain, removing impurities, conditioning and powdering in a mill. The method is characterized in that wheat wetting is achieved under the vacuum condition during conditioning, and more specifically, a vacuum drying oven is adjusted to be at a normal temperature, a proper amount of wheat is obtained through weighing, tap water is added into a dampener, mixed with wheat evenly and placed in the vacuum drying oven, the vacuum degree of the vacuum drying oven is controlled to be 65%-85%, and wheat is taken out after being wetted, tempered and then placed in the mill to be powdered. According to the method, the conditioning state of wheat is changed and the microorganism content in wheat is reduced by means of the vacuum wheat wetting technology, and then the powdering quality and eating quality of wheat are improved. By means of the method, breeding of microorganisms can be inhibited, quick conditioning can be achieved, production of fungaltoxin harmful to health can be reduced, and production efficiency can be improved; furthermore, conditioning warehouse storage capacity can be saved by more than 80%, building investments can be saved greatly, and the composite cost of products can be reduced.