To improve the emulsion properties of soybean protein isolate (SPI), the effect of baicalin (BC) concentrations on the structure, antioxidant properties, and emulsion stability of SPI-BC conjugates were investigated. Structure analysis revealed that BC induced structural depolymerization and unfolding of SPI through the formation of covalent bonds (CN and CS), increasing hydrophilicity, stabilizing the interface, and enabling the formation of smaller oil droplets. The increase in zeta potential of SPI-BC conjugates enhanced electrostatic repulsion between droplets, preventing aggregation, while the strengthened interfacial protein network improved viscosity, shear stress, and thixotropic recovery, thereby significantly stabilizing the emulsion structure. The addition of 0.4 mg/mL BC exhibited the optimal emulsification performance, increasing emulsion stability by 35.4 %. Moreover, SPI-BC emulsions demonstrated enhanced stability against various environmental stressors (storage, heating, pH, ionic strength, and oxidation). These findings confirmed that BC covalent modification enhanced the structural properties of SPI and improved the stability of protein-based emulsions through structural regulation. This study provides new insights into the potential of BC in improving SPI functionality.