The goals of this study were to investigate the effect of preheating conditions on the formation of thermal aggregates of commercial soy isolate protein (SPI) and to characterize the textural properties and microstructure of acid-induced SPI gels. SPI was subjected to preheating treatments at different temperatures (85 °C, 95 °C) and pH values (7.0, 7.5, 8.5, 9.5), and the treated SPI was then used to form acid-induced gels. Characterization of the different gels showed that lower temperatures and pH values favored protein aggregation and the formation of larger aggregates, while higher temperatures and pH values led to a lower degree of aggregation and the formation of smaller aggregates. The lowest average particle size (340.77 nm) and turbidity (0.063), and the highest solubility (81.79 %) were obtained when the preheating temperature of the thermal aggregates was 95 °C and the pH was 9.5. Higher preheating temperature and pH values caused the unfolding of SPI’s tertiary structure, decreased the content of β-sheet structure, and increased the exposure of hydrophobic groups and free sulfhydryl groups. These exposed groups facilitated protein–protein interactions during network assembly, resulting in denser and stronger gel networks. Notably, SPI subjected to higher temperatures and pH values exhibited greater binding capacity for water molecules, higher water holding capacity, and gel strength. Overall, the results showed that modification of preheating temperature and pH can control the formation state of SPI thermal aggregates, ultimately impacting the properties of SPI acid-induced gels.