Salinity is one of the most important factors that influence the physiological status of fish. To adapt to different salinity environments, fish need to consume a lot of energy to maintain osmotic pressure balance. As an intermediate product of lipid metabolism, fatty acids not only play an important role in physiological and biochemical processes, but are also an important energy source for the body. The liver is the main lipid storage organ and the main organ for fatty acid metabolism in fish. is a unique model species to study salinity adaptation because it can live in a wide range of salinities. To investigate the effects of salinity on the metabolism of fatty acids in the liver of , this study compared the changes in fatty acid composition and the mRNA expressions of lipoprotein lipase (LPL), malic enzyme (ME) and peroxisome proliferator-activated receptor-alpha (PPAR-α) in the liver of Nile tilapia in saline water (levels 8 and 16) during a two week salinity stress period. The results showed that the plasma osmolality in the salinity group rose to the highest level in 12 h, and the plasma osmolality in the 16-salinity group was significantly higher than in the 8-salinity group. Meanwhile, the plasma osmolality gradually decreased and tended to be stable in the latter stage of treatments. Before 96 h, the content of saturated fatty acids in the liver of the salinity groups was significantly lower than the freshwater group (<0.05). After 96 h, they gradually recovered to the initial level. The content of monounsaturated fatty acids in the liver of the salinity group was significantly lower than the freshwater group (<0.05). The content of long-chain polyunsaturated fatty acids (mainly docosahexaenoic acid DHA, Eicosapentaenoic Acid EPA, and Arachidonic Acid ARA) in the liver of the salinity groups was significantly higher than the freshwater group (<0.05). The mRNA expressions of LPL, ME, and PPAR-α in the liver of the salinity groups was significantly higher than the freshwater group (<0.05). These results indicate that the composition of fatty acids in the liver and lipid metabolism can be impacted by salinity stress, which provides basic information on lipid energy utilization in fish osmoregulation.