To reveal the nature of thermal aggregation of soybean protein at subunit level, structure and physicochemical properties of αα'- and β-subunits isolated from β-conglycinin, acidic polypeptide, and basic polypeptide from glycinin, as well as β-conglycinin and glycinin, were characterized before and after heat treatment. The transmission electron microscopy (TEM) images showed that β-conglycinin, αα'-subunits and acidic polypeptide formed regular thermal aggregates, which exhibited high solubility, high ζ-potential value, and small particle size. While glycinin, β-subunit, and basic polypeptide aggregated to insoluble clusters with large particle size distribution. The results of size exclusion chromatography and non-reducing electrophoresis showed that the disulfide bond was the important force in stabilizing the protein conformation of thermal aggregates in β-conglycinin, glycinin, and their isolated subunits/polypeptides but β-subunit. The results of surface hydrophobicity and intrinsic fluorescence spectra showed that the thermal aggregations of β-subunit and basic polypeptide were mainly driven by hydrophobic interactions.