The invention discloses a method for preparing fermented milk by separating whey protein by-products through a membrane technology, which belongs to the technical field of production of dairy products. The invention aims to solve the problem of reutilization of byproducts obtained by separating whey protein by the membrane technology. The invention provides the method for preparing the fermented milk by separating the whey protein by-products by using the membrane technology. Wherein the byproducts comprise single cream obtained by centrifugally degreasing fresh milk and a casein solution obtained by microfiltration of the degreased fresh milk, and the preparation method comprises the following steps: mixing the single cream with the casein solution, and adding pectin and sucrose to obtaina mixed solution; preheating, homogenizing, sterilizing and cooling the mixed feed liquid in sequence; and then adding polymerized whey protein and a yoghourt fermenting agent for fermentation, and performing after-ripening so as to obtain the fermented milk. The method can be used for processing set yoghurt.