Free radicles produced by ultrasound were used to produce soy protein isolate (SPI)-cyanidin-3-galactoside conjugates. The conjugation between SPI and cyanidin-3-galactoside was confirmed by the increased ratio of bound polyphenol and the disappearance of cyanidin-3-galactoside's absorption peak in ultraviolet-visible spectrum. Conjugation with cyanidin-3-galactoside resulted in breakdown of SPI aggregate, which also led to a decrease in particle size and an increase in fluorescence intensity. Conjugation disrupted the hydrogen bonds of SPI as indicated by the lowest band intensity at 1646, 1533 and 3300–3450 cm−1 on FTIR spectra. Conjugation also increased the electrostatic repulsion and decreased the hydrophobic interactions between SPI molecules. The SPI-cyanidin-3-galactoside conjugate had higher solubility and less aggregated structure in aqueous medium. The aqueous dispersions and solid powders of these conjugates had better thermal stability than that of SPI.