The invention discloses hypoallergenic soybean peptide whole wheat flour, as well as a preparation method and application thereof. The preparation method comprises the following steps: (1) mixing the soybean protein powder with water to obtain a soybean protein solution, and performing thermal denaturation on the soybean protein solution to obtain a denatured protein solution; (2) adjusting the pH value of the denatured protein solution to 6-9, adding neutral protease and performing first enzymolysis to obtain a first enzymatic hydrolysate; (3) adding alkaline protease and flavourzyme into the first enzymatic hydrolysate to perform second enzymolysis, and performing enzyme deactivation to obtain a second enzymatic hydrolysate; and (4) homogenizing the second enzymatic hydrolysate to obtain the hypoallergenic soybean peptide whole wheat flour. By adopting the preparation method, the sensitization of the soybean protein can be completely eliminated, the utilization rate of the protein is high and the mouth feel of the product is effectively guaranteed, and the prepared hypoallergenic soybean peptide whole wheat flour can be widely used in the milk powder or healthcare product.