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In this study, a novel method called selective proteolysis was applied to the glycinin component of soy protein isolate (SPI), and a degraded glycinin hydrolysate (DGH) was obtained. The effects of high-intensity ultrasound (HIU) treatment (20 kHz at 400 W, 0, 5, 20, and 40 min) on the physical, structural, and aggregation properties of DGH were investigated with the aim to reveal the influence of the selectively hydrolyzing glycinin component on the HIU treatment of soy protein. The effects of HIU on DGH and a control SPI (CSPI) were both time-dependent. HIU induced the formation of soluble aggregates in both samples at an early stage, while it dissociated these newly formed aggregates after a longer duration. Selectively hydrolyzing glycinin contributed to the soluble aggregation by exposing the compact protein structure and producing small protein fractions. The larger extent of hydrophobic interactions and disulfide bonds imparted a higher stability to the soluble protein aggregates formed in DGH. As a result, DGH displayed more ordered secondary structures, a higher solubility, and better gelling properties after the HIU treatment, especially at 20 min. The results of this study will be beneficial to the scientific community as well as industrial application.