Vanillin is widely used in foods, but its poor water dispersibility and limited stability reduce its flavor performance during processing and storage. In this study, soy protein isolate (SPI) was used as a food-grade carrier to prepare soy protein isolate–vanillin (SPIV) complexes via a pH-shifting strategy. SPI and vanillin were first adjusted to pH 9.0, where SPI unfolded and vanillin was deprotonated and dispersed in the solution and then readjusted to pH 7.0 to form SPIV complexes. Vanillin was incorporated into SPI at different loading levels of 0.5, 1.0, 2.5, and 5.0 mg/mL, corresponding to 9–50 wt.% relative to SPI. The binding efficiency of vanillin decreased from 91.03 wt.% to 69.43 wt.% with increasing vanillin loading. Moderate loading preserved the globular morphology of SPI, whereas excessive loading (≥33.33 wt.%) induced vanillin nanocrystal formation and aggregation. Spectroscopic analyses and molecular docking indicated that vanillin interacted with soy proteins through a combination of covalent and noncovalent interactions. Compared with free vanillin, SPIV showed improved color, light, and thermal stability. Among the tested samples, SPIV2 exhibited the most favorable interfacial behavior and application performance, producing more stable emulsions and higher flavor scores in simplified beverage and soy milk models. These findings establish a loading-dependent structure–function relationship in SPIV complexes and provide practical guidance for the design of soy protein-based carriers for flavor stabilization and delivery.