The invention provides special medical infant formula milk powder with yak milk and a preparation method thereof. Each ton of infant formula milk powder comprises the following raw materials: 120-150 kg of yak milk, 80-300 kg of maltodextrin, 40-250 kg of glucose, 150-180 kg of anhydrous milk fat, 60-100 kg of refined vegetable fat, 100-140 kg of whey protein hydrolysate, 10-30 kg of milk protein isolate, and 200-260 kg of white granulated sugar. The yak milk is used as the main raw material to avoid the condition that in exclusive use of common milk, infants need to supplement a large quantity of organic and inorganic nutrients synthesized chemically, so that the yak milk can be absorbed and metabolized well by the infants, the stimulation to the gastrointestinal tract is reduced, the oxidation resistance and the immunocompetence of the human body are enhanced, the oxidative decomposition of fat is promoted, and the human protein synthesis is promoted, and the milk powder plays an important role in promoting the growth and development. The infant formula milk powder uses whey protein and milk protein isolate subjected to enzyme hydrolysis instead of lactose, and the infant formula milk powder is a nutrition specially prepared for infants who are 0-12 months old, lactose-intolerant, and are in diarrhea period and diarrhea recovery period.