Glycinin is one of the important allergens found in soybeans, which can potentially cause severe allergic reactions. Therefore, reducing the antigenicity of glycinin is of major significance to the research of soybean allergies. In order to detect the relationships between the antigenicity and structure of glycinin, samples were extracted from defatted soybean and then processed by ultra-high-pressure combined heat treatments. The processed proteins were determined using SDS-PAGE, enzyme-linked immunosorbent assay (ELISA), immunoblotting, exogenous fluorescence, free sulfhydryl groups and Fourier transform methods. The results revealed that the antigenicity of the processed soy glycinin had decreased. In addition, the content levels of the hydrophobic groups, free sulfhydryl groups, α-helix, β-turn and random coils had increased, and the content of β-sheets had decreased. The results indicated that the reduction in the antigenicity of the glycinin was due to the processing treatments, which effectively destroyed the spatial structure of the glycinin.