The invention provides a special medical food for patients in emergency states and a preparation method thereof. The main raw materials for producing one ton of the product mainly comprise the following components: 100-1500kg of yak milk, 100-2000kg of fresh milk, 200-500kg of whey powder, 50-200kg of refined vegetable oil, 1-100kg of medium chain triglyceride, 1-150kg of white granulated sugar, 1-120kg of lactose, 1-120kg of amino acid, 1-50kg of lactalbumin hydrolysate, 1-120kg of docosahexaenoic acid (DHA), 2-40kg of arachidonic acid (ARA) and 0.1-3kg of casein phosphopeptides. The special medical food is prepared by adding a proper amount of vitamins and minerals or other nutritional ingredients into the yak milk, fresh milk, whey powder, refined vegetable oil, medium chain triglyceride, white granulated sugar, lactose, amino acid, lactalbumin hydrolysate, DHA, ARA and casein phosphopeptides and then processing the raw materials through a physical method, so that the special medical food can meet the demands on various nutritional ingredients of the crowd suffering from malnutrition, protein deficiency, wounds with toxin accumulation and high catabolism, infection, operation and other stress states.