The invention discloses a preparation method of small-molecule panax notoginseng polysaccharide extract. The preparation method includes: using panax notoginseng as the raw material, crushing the raw material, extracting with an ethanol solution, extracting panax notoginseng residues with water obtain crude panax notoginseng polysaccharide extract, performing ethanol precipitation, dissolving precipitate with water, and then adding trifluoroacetic acid or lysozyme to perform hydrolysis to obtain crude small-molecule polysaccharide liquid; using a cation-anion exchange column to remove the protein, pigment and the like of the crude small-molecule polysaccharide liquid, using activated carbon powder for decoloring, filtering with a titanium-bar filter to obtain a colorless low-viscosity small-molecule polysaccharide solution, concentrating, and performing freeze drying to obtain the small-molecule panax notoginseng polysaccharide extract. The preparation method has the advantages that the method is simple to operate, low in cost and high in industrialization degree; the small-molecule panax notoginseng polysaccharide extract can promote macrophage proliferation, further differentiation and maturation of macrophage can be achieved to obtain activated macrophage, and the phagocytic ability of the macrophage can be evidently enhanced; fast increasing of cell immunity during a cell culture immunity test can be achieved; the extract has application prospect in immunological disease treatment, and the preparation method is suitable for industrial production.