The effects of three different enzyme treatments on the structure and volatile compounds of egg yolk protein were investigated. The secondary and tertiary structures, as well as volatiles, were characterized using ultraviolet spectroscopy (UV), fourier transform infrared (FTIR) spectroscopy, free sulfhydryl group analysis, and gas chromatography-mass spectrometry (GC-MS). FTIR analysis revealed a decrease in the contents of intermolecular, intramolecular, and intermolecular antiparallel β-sheets while an increase in random coils was observed. The contents of α-helices and β-turns did not show significant changes, indicating a reduction in protein compactness. Enzymatic treatment led to an increase in hydrophobic interaction, electrostatic interaction, and hydrogen bond formation within the egg yolk hot gel (EYG). Structural characterization demonstrated that EYG formed large uniform air chamber cavities after lipase hydrolysis (LEYG), while EYG hydrolyzed by papain (PEYG) and by flavor protease (FEYG) exhibited more compact structures. In addition, the binding of proteins to flavor substances inhibited the release of volatile flavor compounds. These findings provide insights into enhancing the flavor and texture of egg yolk by modulating its protein structure.