The invention discloses double-protein yoghourt cheese and a preparation method thereof, and belongs to the technical field of food. Milk protein and soybean protein are selected as raw materials, antioxidant active peptide solutions of the soybean protein and whey protein are respectively prepared by adopting a high-pressure homogenization method, the antioxidant active peptide solutions are prepared into yoghourt, and the cheese is prepared on the basis of the yoghourt. Three probiotics, namely Bifido, Dophilus and Protect, are added into the yoghourt, and the three probiotics can maintain and improve the intestinal flora balance of a human body from three different aspects, so that the intestinal health and the immunity of the organism are improved, and the yoghourt is particularly suitable for people with sensitive intestinal tracts to eat. The food not only can meet the requirements of people at different age stages on nutrients such as protein, calcium, vitamins, dietary fibers and the like, but also has certain effects of inhibiting obesity, reducing cholesterol and preventing chronic diseases. In addition, the two proteins are treated by adopting an advanced technology of high-pressure homogenization, so that the interaction of the two proteins is facilitated, and the functional properties of the product can be improved.