Microbial transglutaminase (mTG) is most frequently utilized in order to increase the gelling properties of soybean protein isolate (SPI), but there are still some limitations of mTG-based hydrogel fabrication technology. Therefore, we aimed to develop a dual modification technique based on enzyme plus organic acid treatment to fabricate SPI hydrogels with high gel strength and stability. Our results showed that mTG plus glucose-δ-lactone (GDL), lactobionic acid (LBA) or maltobionic acid (MBA) treatment could significantly improve the gel strength, textural properties, and water-holding capacity of SPI hydrogels. Also, the addition of these organic acids remarkably reduced the surface hydrophobicity (H) and intrinsic fluorescence as well as increased the storage modulus (G'), loss modulus (G″) values, average particle size, and the absolute value of zeta potential of samples. GDL, LBA, or MBA greatly increased the β-sheet level and decreased the α-helix level in hydrogels, as well as dissociated 11S subunits of SPI into 7S subunits. Notably, covalent interactions, hydrogen bonding, and hydrophobic interactions of three organic acids with SPI, as well as the effects of organic acids on the interactions among the intramolecular and intermolecular forces of SPI molecules, contributed to their promoting effects on the formation of hydrogels. The LF-NMR and SEM analyses confirmed the effects of GDL, LBA, and MBA on converting the free water into immobilized and bound water as well as forming a dense stacked aggregate structure. Therefore, GDL, LBA, and MBA are promising agents to be combined with mTG in the fabrication of SPI hydrogels with high gel strength and stability.