This study evaluated the effects of d-galactose (DG) concentration on the functional characteristics, physicochemical properties, structure and non-covalent binding ability of pH shifting treated soybean glycinin (S–11S). Multispectral and microscopic imaging analysis showed that the pH shifting induced soybean glycinin self-assembly into more stable small particle size aggregates, and the functional properties of S–11S were significantly enhanced. The introduction of DG further enhances the functional properties of S–11S, and the solubility and emulsification activity of the composite system are inversely proportional to the concentration of DG. In order to clarify the reason for the change, multispectral analysis found that the tertiary structure of S–11S was de-folded and the disordered structure was increased, which induced S–11S and DG to form smaller and stable nanoparticles than S–11S through hydrophobic forces and hydrogen bonding, and the optimal binding ratio was 10.8:1. In addition, the simulation results of molecular dynamics and molecular docking are in agreement with the experimental results. Therefore, the addition of DG can stabilize the overly discrete S–11S conformation and improve its functional characteristics. These results provide a theoretical basis for the application of modified protein and monosaccharide composite products in food and materials.