The emulsification of vegetable protein is closely related to solubility. The purpose of this study was to evaluate the effect of ultrasound on protein emulsification and to provide a prospective method for assessing the digestive properties of emulsions. In this article, we investigate the emulsion stability of ultrasonic pretreated soy protein isolate (SPI), and its three storage proteins, namely β-conglycinin (7S), lipophilic protein (LP), and glycinin (11S), under dynamic gastric conditions. The effects of these emulsions on lipolysis during digestion in the small intestine are also assessed using an in vitro dynamic human stomach simulator and a small intestine model. Particle size and ζ-potential measurements, as well as confocal laser scanning microscopy, revealed that during dynamic gastric digestion, the flocculation degree and floc size of 7S and soybean LP emulsions are larger than that of 11S and SPI emulsions. Meanwhile, ultrasound pretreatment of the proteins was found to prevent the agglomeration of the emulsion in a dynamic gastric environment. Moreover, enhanced flocculation delayed oil droplet delivery to the small intestine and subsequently retarded the release of lipophilic nutrients. The droplet size, molecular weight, and protein secondary structures of the ultrasonicated proteins were conducive to relatively higher rates and degrees of lipolysis in intestinal digestion than those of unsonicated proteins. Additionally, the slow-release effect of LP was superior to that of 11S and SPI, whereas 7S was comparatively more difficult to digest. The present study elucidated the fate of soy protein in the digestive tract and may facilitate microstructural food design to regulate physiological responses during digestion.