The present invention provides a soybean oligopeptide with low allergenicity and little bitterness and its preparation method and application. The preparation method includes the following steps: 1) mixing a soybean protein powder with water to obtain a soybean protein solution, and then performing thermal denaturation on the soybean protein solution, to prepare a denatured protein solution; 2) adjusting pH value of the denatured protein solution to 6-9, and then adding a neutral protease and papain to conduct a first enzymolysis, to obtain a first enzymatic hydrolysate; 3) adding an alkaline protease and a flavor protease into the first enzymatic hydrolysate to conduct a second enzymolysis, and after performing enzyme inactivation, to obtain a second enzymatic hydrolysate; and 4) centrifuging the second enzymatic hydrolysate, and performing membrane filtration on centrifuged supernatant liquid, to obtain the soybean oligopeptide with low allergenicity and little bitterness.