The invention provides a method for extracting small molecule mushroom polysaccharide with microelement-enriched deuterium-depleted water. By means of the low deuterium characteristic of glacier water, the glacier water serves as an extraction solvent, and due to the fact that the glacier is rich in microelement, dissolution and extraction of the mushroom polysaccharide are facilitated; in the extraction process, the deuterium-depleted water is heated, microwave extraction is cooperated, the extraction efficiency of the polysaccharide is improved conveniently, and the extraction rate of the polysaccharide is higher; after extraction, repeated freezing and thawing are conducted first, protein and other impurities are removed, the protein is further removed by means of trypsin, the polysaccharide acquisition rate is increased, final alcohol sedimentation is conducted once, and the protein can be efficiently removed; finally, trifluoroacetic acid is added, the mushroom polysaccharide is cut to be small molecule polysaccharide, human body absorption is facilitated, and health-care value is improved. The polysaccharide has the effects of inhibiting cancer cells, lowering blood fat, lowering blood glucose and the like. Compared with the prior art, according to the method, the polysaccharide extraction rate is high, few impurities exist, polysaccharide molecules are small, and human body absorption is facilitated.