The effects of combined treatment of ultrasound and basic amino acids (BAA) on the structural and functional properties of soy isolate protein (SPI) were studied, and correlation analyses were investigated. The results showed that combined treatment was more effective in improving the emulsification and solubility of SPI than that of BAA treatment alone. The ζ-potential result showed that the synergistic effect of ultrasound and BAA enhanced the ζ-potential of SPI compared to BAA treatment alone, which improved the electrostatic repulsion between the protein molecules. The surface hydrophobicity and fluorescence spectrum results showed that more hydrophobic groups were exposed to the polar environment, which promote the hydrophilic-hydrophobic groups balance. The free sulfhydryl groups and total sulfhydryl results illustrated that combined treatment was more effective in increasing the content of free sulfhydryl groups and decreasing total sulfhydryl content. The results of secondary structure content showed that the combined treatment was more conducive to the transformation of SPI to ordered molecular structure. SDS-PAGE results showed that neither ultrasound nor BAA treatment could change the structure of SPI subunits. Correlation studies showed that surface hydrophobicity was positively correlated with solubility (0.960) and emulsification (0.861). The ζ-potential was highly significantly negatively correlated with solubility (-0.974).