The oxidation-induced phospholipids (PLs) underwent structural and compositional analysis, alongside the establishment of a simulation system to verify the link between phospholipid oxidation and flavor substances formation in sturgeon caviar. Structural alterations of PLs were tracked using 31P and 1H nuclear magnetic resonance (NMR), electron spin resonance spectroscopy (ESR), and Raman spectroscopy. The findings revealed a reduction in phosphatidylcholine (PC) and phosphatidylethanolamine (PE) from 82.3% and 10.4% to 58.2% and 5.8% respectively. Free radical signals exhibited an initial increase followed by a decrease. The diminished intensity in Raman spectra at 970 and 1080 cm−1 indicated reduced fat unsaturation attributable to PLs oxidation. Correlation analysis highlighted a significant association between PC and PE containing C22:6, C20:5, C20:4, and C18:2 with flavor substances, suggesting their role as key precursors for flavor development. This study established a theoretical basis for understanding the change of flavor quality in sturgeon caviar during storage.