The invention discloses flatulence factor-free soybean milk and a preparation method thereof. The preparation method comprises the following steps: soaking high-quality soybeans for 6-12 hours, draining, crushing into 100-300-mesh micropowder, proportionally adding warm boiled water with the temperature of 50-60 DEG C, adding 10-20 U/ g of alpha-galactosidase, uniformly stirring and preserving the temperature for 30-45 minutes, and stewing at high temperature till the soybeans are well-cooked. The flatulence factor-free soybean milk provided by the invention is whole-nutrition soybean milk which is economical, good in quality, fast to process, sweet in taste, easy to digest and absorb and rich in nutrient, can meet requirements of families and food and beverage enterprises and can meet demands of people on health.