This study aimed to illustrate the relationship among physicochemical properties, subunit composition and protein functionalities in a broad collection of commercial soy protein isolates (SPIs) from China and the EU. The results indicated that SPIs had large variations in glycinin/β-conglycinin composition, protein denaturation, and water- and oil-binding capacity (WBC and OBC) and solubility. These SPIs could be roughly divided into pre-denatured SPI, partially hydrolyzed SPI, and less modified SPI. The pre-denatured SPI with high surface hydrophobicity and large particle sizes showed reduced WBC and OBC due to increased protein aggregation, and partially hydrolyzed SPI showed high protein solubility owing to the exposure of hydrophilic regions and reduction in molecular size. The processing-induced physicochemical changes played a pivotal role in determining protein functionalities, whereas subunit composition affected protein functionality less. Overall, this study highlighted the obvious difference in raw material quality of commercial SPI, and provided promising methods for SPI categorization.