To investigate the interaction mechanism between bovine protein β-lactoglobulin (β-LG) and theaflavin (TA), chlorogenic acid (CA) and delphinidin-3-O-glucoside (D3G), multi-spectrometry analytical methods and molecular modeling were applied. Fluorescence experiments proved that polyphenols strongly quenched the intrinsic fluorescence of β-LG mainly through static quenching and the main interaction force was hydrophobic interaction. Moreover, Fourier transform infrared (FTIR) and circular dichroism (CD) indicated that polyphenols changed β-LG secondary and tertiary structure. Enzyme-linked immunosorbent assay and molecular modeling study manifested that complex of β-LG with polyphenols could significantly reduce the IgE-binding capacity of β-LG due to the polyphenol binding site directly obscures the IgE linear epitopes. In conclusion, polyphenols had impact on the structure and potential functionality of β-LG, which would be valuable in dairy processing industry and food nutrition security.