This study explored the Maillard reaction process during the glycation of soy protein isolate (SPI) with galacto-oligosaccharides (GOSs) under high-pressure homogenization (HPH) and its effects on the emulsifying properties of SPI. SPI-GOS glycation under moderate pressure (80 MPa) significantly inhibited the occurrence and extent of the Maillard reaction (p < 0.05), but homogenization pressures in the range of 80–140 MPa gradually promoted this reaction. HPH caused a decrease in the surface hydrophobicity of the glycated protein, an increase in the abundance of free sulfhydryl groups, unfolding of the protein molecular structure, and the formation of new covalent bonds (C=O, C=N). Additionally, the particle size of emulsions created with SPI-GOS conjugates was reduced under HPH, thus improving the emulsifying properties of SPI. A reduction in particle size (117 nm), enhanced zeta potential (−23 mV), and uniform droplet size were observed for the emulsion created with the SPI-GOS conjugate prepared at 120 MPa. The conformational changes in the glycated protein supported the improved emulsification function. All results were significantly different (p < 0.05). The study findings indicate that HPH provides a potential method for controlling glycation and improving the emulsifying properties of SPI.