The invention relates to a method for processing soybean isolated protein by utilizing a biological enzyme technology. The method comprises the following steps of: during preparation, selecting high-quality soy protein isolate, and dissolving; performing thermal denaturation; adjusting the pH value to 8.0 to 9.0; adding composite hydrolase of alkali protease, neutral protease, papain and trypsin, and reacting for 2 to 3 hours; adjusting the pH value to 4.0 to 6.0; inactivating enzyme; when cooling to a temperature below 50 DEG C, adding filter aid enzyme; collecting filtrate to dissolve filter residues; adding composite hydrolase of acidic protease, neutral protease, papain and trypsin, and reacting for 1 to 2 hours; inactivating the enzyme; when cooling to temperature of below 50 DEG C, adding the filter aid enzyme; filtering by a paperboard; performing ultrafiltration; drying by microwaves under vacuum; and crushing and sieving. The soybean polypeptide powder prepared by the method can improve the solubility of albumen powder to a maximum limit and keep the color and luster of appearance, mouthfeel, flavors and the bioactivity of active ingredients, offers a good mouthfeel, is easy to absorb and can be widely applied to industry of dairy products, drinks and health-care products.