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Structural changes of soybean protein-phosphatidylcholine complex under ultrasonic treatment and high pressure homogenization by Raman spectroscopy were analyzed. Ultrasonic treatment and high pressure homogenization treatment both were found increased the content of α-helix and random coil structure, but decreased the β-structure of soybean protein. The interaction of soybean protein and phosphatidylcholine significantly decreased the protein α-helix structure by transforming it into random coil and β-sheet structures. Under ultrasonic treatment and high pressure homogenization, the protein α-helix structure of soybean protein-phosphatidylcholine complex was lower than that of the high speed dispersion treatment complex, while the content of β-folded structure and random coil structure were higher. Tryptophan and tyrosine residues of soybean protein tended to expose with ultrasound and high pressure homogenization, which promoted the hydrophobic interaction between soybean protein and phosphatidylcholine. The interaction sites were located in soybean protein hydrophobic amino acid side chain and phosphatidylcholine lipid hydrophobic chain, the hydrophobic interaction was the main force of soybean-phosphatidylcholine interaction. Under the condition of ultrasonic treatment and high pressure homogenization, the structure of disulfide bond of soybean protein was not changed significantly, and the gauche-gauche-trans conformational vibration mode was remained. The interaction of soybean protein phosphatidylcholine did not change the structure of disulfide bond.