Bacillus subtilis is the primary strain used in fermented soy products. The applicant fermented soymilk with the laboratory strain B. subtilis BSNK-5 to enhance nutrient density. However, prolonged fermentation caused rapid deterioration in flavor, resulting in an off-flavor poorly accepted by consumers, limiting its industrial application. Studies identified isovaleric acid (IVA), isobutyric acid (IBA), and 2-methylbutyric acid (2-MBA) as the main off-flavor compounds. The mechanism controlling off-flavor release remains unclear. Therefore, soybean protein was used as a model to investigate off-flavor release by analyzing binding percentage, physicochemical properties, conformation, and interaction forces. The modification of off-flavor by phenolic compounds was also examined. Results showed that soybean protein bound over 90 % of the flavor compounds, including a 98.6 % binding rate for IVA. Binding between soybean protein and off-flavor compounds was confirmed by the formation of large aggregates, decreased surface hydrophobicity, and a structural transformation from α-helix to β-sheet. Hydrogen bonds and hydrophobic interactions were identified as the primary interaction forces. Adding phenolic compounds significantly reduced soybean protein binding to flavor compounds. Phenolic compounds had a stronger binding affinity to soybean protein compared to flavor compounds and occupied binding sites on soybean protein, preventing flavor compound binding. L-epicatechin, (-)-epicatechin gallate, and epigallocatechin-3-gallate primarily occupied binding sites for 2-MBA, while ferulic acid, chlorogenic acid, and caffeic acid occupied sites for IVA, IBA, and 2-MBA. This research aids in controlling flavor release by soybean protein in food systems, supporting the development of nutrient-rich fermented foods.