To investigate the effect of high-pressure homogenization on the structure and emulsification of soybean protein, high-pressure homogenization (HPH) treatment at 20min and 100℃ were applied to the soybean protein thermal aggregates (HSPIs). The changes of HSPIs structure characteristics (particle size distribution, turbidity, skeleton structure, secondary and tertiary structure, hydrophobicity, potential, sulfhydryl) and emulsification characteristics (rheological characterization, emulsification and emulsification temperature) were assayed. The results showed that compared with the heat soluble aggregates degree, the lower pressure of HPH can promote the re-aggregation of the thermal induced HSPIs, which resulted in the increase of particle size and turbidity, the densification of HSPIs skeleton structure. Along with the re-aggregation, the HSPIs disordered structure, particle ζ-potential and protein peptide chains disulfide bond content were increased, and resulted in the increase of emulsifying activity and decrease of hydrophobicity. While on HPH, strong strength homogenization can lead the disulfide bond and skeleton structure of HSPIs broken, the protein spatial structure was opened, and the hydrophobic sites were exposed, which resulted in enhancement of hydrophobicity, shortening of protein peptide chain, decrease of particle size and the increase of ζ-potential, and then the decrease of emulsifying activity of HSPIs. The results for the modification of soybean protein functional properties and the application by high-pressure homogenization changed HSPIs.