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In response to digestion complex environments, protein's ability to bind bile salts (BS) will be altered. This study aimed to assess the different effects of in vitro digestion on the BS-binding capacity of fermentation-organic acid compound-modified and unmodified WPI. According to the results, modified WPI can increase the degree of hydrolysis, reduce the sulfhydryl group content, and expose aromatic amino acids during digestion, indicating that the BS-binding ability of WPI is dependent on the hydrogen bond content. The more residual of surface hydrophobicity and β-sheet and β-turn contents suggested that exposure of hydrophobic groups of modification would promote BS-binding with hydrophobic of modified WPI in simulated digestion, consistent with the change in sulfhydryl content and surface hydrophobicity. This further confirms the higher binding ability of WPI for BS through hydrophobic interactions. In addition, the apparent viscosity and viscoelasticity of modified WPI were increased, which contributed to improved BS binding. Further, the modification enhanced the content of fragmented polymers with a molecular weight less than or equal to 3.3 kDa after digestion. Based on peptidomics, it was concluded that FLPYPYYAKP and ALKALPMHIRL were polypeptides with strong cholesterol-lowering effects, with a significant difference between modified and unmodified WPI. • Residual tyrosine and tryptophan side chains of modified WPI promoted BS binding. • Viscosity and viscoelasticity of the modified WPI was beneficial to BS binding. • Modification enriched the content of fragmented polymers (≤3.3 kDa MW) and hydrophobic amino acids after digestion. • Cholesterol-lowering peptides of FLPYPYYAKP and ALKALPMHIRL were improved by modification after in vitro digestion. [ABSTRACT FROM AUTHOR]