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The Pacific white shrimp ( Litopenaeus vannamei ), a euryhaline penaeid species, can tolerate a wide range of salinities, but little is known on its strategies to cope with low salinity fluctuations from the aspect of lipidomics. Thus, in this study,  L. vannamei  were grown in two different salinities [3 and 30‰ (control)] for 8 weeks, and then an liquid chromatography (LC)–mass spectrometry (MS)-based lipidomics analysis was performed to reveal the lipid profile differences in gill and muscle.  L. vannamei  under low salinity had lower weight gain and condition factor than the control shrimp at 30‰, but no differences were found in survival and hepatopancreas index. A higher number of differential lipid metabolites were identified in gill than in muscle in  L. vannamei  at salinity 3‰ relative to the control shrimp at salinity of 30‰ (159 versus 37), which belonged to 11 and 6 lipids classes, respectively. Of these lipids, phosphatidylcholine (PC), phosphatidylinositol (PI), phosphatidic acid (PA), phosphatidylethanolamine (PE), and triglyceride (TG) were the main lipids in both shrimp gill and muscle, regardless of salinities. Compared with the control shrimp at salinity 30‰, the percentage of PC significantly reduced, but TG and PA significantly increased in gill of shrimp at salinity 3‰. Moreover, the relative fatty acid abundances showed significant changes in  L. vannamei  between the two salinity groups, but the patterns of the changes were complex and were fatty acid dependent. Neither lipid nor fatty acid composition in muscle was affected by salinity. Further pathway analysis showed that these metabolites were closely related to lipid and fatty acid metabolic pathways. All the findings in this study reveal that the lipid variations are closely related to bio-membrane structure, mitochondrial function, energy supply, or organic osmolyte contents in hemolymph for improving osmoregulatory capacity of  L. vannamei  under low salinity.