The Pacific saury (Cololabis saira) is a highly nutritious deep-sea fish, rich in omega-3 polyunsaturated fatty acids (n-3 PUFAs). This study comprehensively investigated fatty acids composition and lipid profiles of different parts of Pacific saury based on an untargeted lipidomic strategy. Results suggested that the crude fat content of meat, head and viscera were 5.81%, 10.90%, and 19.46%, respectively. The contents of PUFAs were 41.08%, 34.96% and 33.14%, respectively. Among them, the n-3 PUFAs in the head (34.58%) were significantly higher than meat (29.40%) and viscera (27.95%). Moreover, 5752 lipid molecules were identified, where glycerophospholipids (GP) were the most numerous lipid type (45.58%), with phosphatidylcholine (PC) being main differential subclass. PC (20:3_22:6) was the most abundant molecule in the head (14.59%) and meat (19.60%). Head_vs_viscera group had higher characteristic PC abundance. This study will provide a theoretical basis for the physiological activity and lipid high-value utilization of Pacific saury.