The invention discloses a method for preparing a compound protein emulsifying system, which belongs to a processing technology of plant and animal proteins. The method comprises the following steps: (1) mixing soy protein isolate with water to obtain a soy protein solution, and regulating the pH of the protein solution to neutral; (2) heating the neutral soy protein solution for modification, and freeze drying the neutral soy protein solution after the heating modification procedure to prepare modified soy protein isolate; (3) leaching griskin, centrifuging and filtering the leached griskin to obtain myofibrillar protein, mixing the modified soy protein isolate with the myofibrillar protein, dissolving the mixture in a phosphate buffer containing sodium chloride to prepare a mixed protein solution; (4) adding vegetable oil in the mixed protein solution to obtain a protein-grease mixed solution; and (5) homogenizing the protein-grease mixed solution to obtain the compound protein emulsifying system. The soy protein and myofibrillar protein compound emulsifying system prepared by the method has high emulsifying capacity and good emulsifying stability, and the soy protein and myofibrillar protein compound emulsifying system can be applied in emulsified sausage products to reduce the cost and improve the nutritional value.