Ultrasound treatment and high-pressure homogenization were used to prepare soybean protein (SP)-phosphatidylcholine (PC) nanoemulsions in this study. Nanoemulsions prepared by high-pressure homogenization were more stable. The structural changes of SP and PC under ultrasound treatment and high-pressure homogenization treatment were investigated by Raman spectroscopy. It could be concluded that ultrasound and high-pressure homogenization treatments increased both the content of α-helix and unordered structure but decreased that of β-structures of SP, while the interaction between SP and PC decreased α-helix content and also reduced unordered structure and β-sheet structure. Ultrasound treatment and high-pressure homogenization exposed more tryptophan and tyrosine residues to promote hydrophobic interaction between SP and PC, which was beneficial for stabilizing the nanoemulsion. The SP-PC interaction exerted a more significant effect on side chain structure than those observed under ultrasound treatment and high-pressure homogenization. The dominant g-g-t vibrational mode of the disulfide bond of soybean protein was not appreciably changed by the two preparations. High-pressure homogenization increased the disorder of lipid chains of PC, promoting SP-PC interaction and thereby increasing the stability of the nanoemulsion. The structural change provided a theoretical basis for preparation of two nanoemulsions.