The invention relates to a method for preparing a high-purity soybean oligosaccharide from soybean whey wastewater, which comprises the following steps: (1) preprocessing of raw materials: heating soybean whey wastewater or soybean molasses diluent obtained from an industrial production in water bath to 10 to 80 DEG C, and pre-clarifying and filtering the heated product with a microfiltration membrane and/or an ultra-filtration membrane; (2) an enzymolysis process: adding enzyme into the filtrate of the soybean whey wastewater or the soybean molasses diluent obtained in step (1), stirring the obtained product at a speed of 50 rpm for 1 to 3 min, regulating the pH value to be 3 to 11, reacting the obtained product at the temperature of 0 to 60 DEG C for 10 min to 12 h, and then, inactivating the obtained product in boiling water bath for 10 to 15 min to obtain enzyme-inactivated solution; and (3),a nanofiltration and separation process: filtering the enzyme-inactivated solution with an ultra-filtration membrane again to remove enzyme, and then filtering and separating the obtained solution with a nanofiltration membrane to obtain nanofiltration concentrated solution, which is oligosaccharide solution. Compared with the prior art, the total amount of cane sugar, fructose, glucose and other monosaccharide in the prepared product does not exceed 5%, so that the technology is suitable for industrial mass production.