The present study aims to investigate the effects of ultrasound on the non-covalent interaction of β-lactoglobulin (β-LG) and luteolin (LUT) and to investigate the relationship between allergenicity and human intestinal microbiota. After treatment, the conformational structures of β-LG were changed, which reflected by the decrease in α-helix content, intrinsic fluorescence intensity and surface hydrophobicity, whereas the β-sheet content increased. Molecular docking studies revealed the non-covalent interaction of β-LG and LUT by hydrogen bond, van der Walls bond and hydrophobic bond. β-LG-LUT complex treated by ultrasound has a lower IgG/IgE binding ability and inhibits the allergic reaction of KU812 cells, depending on the changes in the conformational epitopes of β-LG. Meanwhile, the β-LG-LUT complex affected the composition of human intestinal microbiota, such as the relative abundance of Bifidobacterium and Prevotella. Therefore, ultrasound improved the non-covalent interaction of β-LG with LUT, and the reduction in allergenicity of β-LG depends on conformational epitopes and human intestinal microbiota changes.