• Six flavonoids reduced the antigenicity of β-LG by noncovalent interaction. • Structures of β-LG experienced distinct changes due to noncovalent interaction. • We explored the binding patterns of flavonoids and β-LG by molecular docking. • The flavonoids bound to the epitope regions of β-sheet and β-turn in β-LG. It is practical to inhibit the allergenicity of β-lactoglobulin (β-LG) using natural products acting via noncovalent interactions; however, the mechanism of the effect has not been investigated in detail. Herein, the comprehensive noncovalent mechanism of inhibition of the antigenicity of β-LG by six flavonoids (kaempferol, myricetin, phloretin, epigallocatechin-3-gallate (EGCG), naringenin, and quercetin) was investigated by spectroscopic and molecular docking methods. Our results indicate that six flavonoids reduced the antigenicity of β-LG in the following order: EGCG > phloretin > naringenin > myricetin > kaempferol > quercetin, with antigenic inhibition rates of 72.6%, 68.4%, 59.7%, 52.3%, 51.4% and 40.8%, respectively. Six flavonoids induced distinct conformational changes in β-LG, which were closely associated with a decline in antigenicity of β-LG. The flavonoids bound to specific antigen epitopes in the β-sheet and β-turn of β-LG to induce a decrease in the antigenicity of the protein. [ABSTRACT FROM AUTHOR]