background: Acid and thermal stabilities are important properties for the preparation of acidic protein beverage. It is an important method for enzymatic modification to improve the functional properties of protein. Irpex lacteus protease showed a selectively hydrolysis to soy proteins. The purpose of this study was to investigate the mechanism of enzymatic hydrolysis and its effects on acid and thermal stabilities of soy proteins. results: The Irpex lacteus protease selectively hydrolyzed the α and α' subunits of the native soybean β-conglycinin (7S globulin) to produced products which presented as the 55 kDa band on the SDS-PAGE (Sodium dodecyl sulfate polyacrylamide gel electrophoresis). The amino acid sequences of 55 kDa polypeptides were analyzed in gel multi-enzyme digestion followed by LC-MS/MS (Liquid chromatograph-mass spectrometer). By matching the multi-enzyme digestion peptides with the published polypeptide chain sequences of the α and α' subunits, it was confirmed that the 55 kDa polypeptides were formed by eliminating amino acid residues in both sides of N- and C-terminals. From the published protein structure database (https://www.uniprot.org/), it is known that the cleaved peptide bonds were in extension regions. Non-selective enzyme hydrolysis of both β-conglycinin (7S globulin) and glycinin (11S globulin), with the corresponding drastic increases in the degree of hydrolysis, was observed when the substrates were preheated to the denaturation degree of 40% and above. However, 55kDa hydrolyzed products and B polypeptides showed some extent of resistance to the proteolysis by Irpex lacteus protease even if denaturation degree was 100%. Both selective and non-selective hydrolysis of soy proteins by Irpex lacteus protease improved the acid and heat stabilities under the same hydrolysis conditions (E/S, time and temperature). conclusions: Enzymatic hydrolysis of soybean proteins by the Irpex lacteus protease can effectively improve the acid and thermal stabilities of proteins. This discovery is significant to avoid aggregation during the process of beverage industry. In the near future, the protease has potential application value for modification of other proteins. This article is protected by copyright. All rights reserved.