It is practical to inhibit the allergenicity of beta-lactoglobulin (beta-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 beta-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 beta-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 beta-LG, which were closely associated with a decline in antigenicity of beta-LG. The flavonoids bound to specific antigen epitopes in the beta-sheet and beta-turn of beta-LG to induce a decrease in the antigenicity of the protein.