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This study aimed to explore the effect of ultrasound-assisted pH shift on the structural and functional properties of soybean lipophilic proteins (SLP). SLP were modified under ultrasound (240 W, 20 min) and extreme pH (pH 1 or 12) conditions. The primary, secondary and tertiary structures of native and modified SLP were characterized by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), free sulfhydryl content, Fourier transform infrared (FTIR) spectroscopy, and fluorescence spectroscopy, and their functional properties were analyzed. The results showed that ultrasound-assisted alkaline pH shift resulted in the greatest changes in the structural and functional properties of SLP. The average particle size of SLP decreased from 5 245.33 to 447.13 nm, the ζ-potential value decreased from − 5.95 to − 18.53 mV, the free sulfhydryl content decreased, the α-helix content increased, and the fluorescence spectrum exhibited a blue shift and a decrease in fluorescence intensity. In addition, the solubility increased from 9.84% to 92.04%, and the emulsifying and foaming properties increased. Therefore, ultrasound and pH shift treatments have a synergistic effect on the structural and functional properties of SLP, and they are closely correlated with each other.