A fast and efficient shotgun lipidomics strategy was applied to analyze phospholipids (PL) in the oyster Crassostrea plicatula, including 29 species of phosphatidylcholine (PtdCho), 23 species of phosphatidylethanolamine (PtdEtn), 11 species of phosphatidylserine (PtdSer), 6 species of phosphatidylinositol (PtdIns), and 17 species of lysophospholipids (Lyso-PL). During storage at 4 °C for 7 days, the PL content decreased by 68.08%, but a significant increase in the FFA content was observed (from 63.11 to 318.72 μg/g). PtdCho and PtdIns decreased relatively by 64.97 and 67.49%, and PtdSer decreased most markedly by 74.15%. However, the PtdEtn content increased slightly during the early stages of storage but subsequently began to decrease. Moreover, PL with eicosapentaenoic acid (EPA-PL) and docosahexaenoic acid (DHA-PL) decreased by 51.77 and 50.61%, whereas plasmalogens were relatively stable showing only a 25.46% decrease. In particular, through enzyme activity analysis of lipase, phospholipase A (PLA), phospholipase A (PLA), phospholipase C (PLC), and phospholipase D (PLD), it was observed that the activities of all these enzymes increased at the early stage at 4 °C, but their activities were at lower levels when the oysters were stored at -20 °C. During the storage period at 4 °C, correlation analysis suggests that the degradation of PtdCho was mostly correlated to PLA (p < 0.05), whereas PtdEtn and PtdSer were more markedly correlated to lipase and PLD, respectively. The above result indicates that the hydrolysis mechanism of PL during seafood storage was correlated to the lipid hydrolytic enzyme activities under different storage temperatures.