The invention discloses a method for reducing allergenicity of special soybean isolation protein of soy-based infant formula powder, belonging to the field of food safety. Soybean isolation protein prepared from non-transgenic and non-radiation soybean is used as the raw material; the special soybean isolation protein is subjected to compound modification by adopting an ultra-high static pressurenon-thermal physical method cooperatively with a compound enzyme method, therefore, the allergenicity of the special soybean isolation protein is obviously reduced; meanwhile, functionalities, such as an nitrogen soluble index, emulsifying activity, viscosity, thixotropy, in-vitro digestibility coefficient and the like, and nutritional quality are improved. Detailed parameters of the ultra-high static pressure and compound enzyme enzymatic treatment are as follows: weighing a certain amount of the soybean isolation protein, mixing and modulating the soybean isolation protein into 1-1.65% of uniform slurry, then, transferring the slurry into an aluminium foil bag, sealing, and vaccumizing; pre-heating an ultra-high static pressure water bath circulation device to 20-25 DEG C, then, puttingthe soybean isolation protein in an ultra-high static pressure processing cavity, increasing pressure to 315-385 MPa with the pressure increasing rate of 250 MPa/min, and keeping the pressure for 15-20 min with the pressure relieving rate of 300 MPa/min; and concentrating a soybean isolation protein solution in vacuum to 5-15%, then, transferring the soybean isolation protein solution into an enzymatic tank, adjusting the temperature of enzymatic liquid to 48-55 DEG C, adjusting a pH value of the enzymatic liquid to 6-7.5, wherein the use amount of special compound enzyme (preparing neutral protease and flavourzyme according to the mass ratio of 1:1 in a mixed and compound manner) is 1.5-2.5%; and the enzymatic time is 1.2-2.5 h; and then, obtaining a finished product by enzyme inactivating the enzymatic liquid, desalting, concentrating, atomizing and drying. When the product obtained by using the method disclosed by the invention is detected by ELISA (Enzyme-Linked Immuno Sorbent Assay), the allergen content is reduced by 87.49-90.75%.