Salinity is one of the most important abiotic factors in aquaculture, which greatly affects the physiology and metabolism activity, growth, development, production, and immune of marine fish. Greater amberjack has the characteristics of fast growth and short breeding cycle, and is one of the important export aquatic products in China. In this study, we used RNA-seq technology to identify and characterize acute salinity-stress-induced genes expression in greater amberjack liver tissue, and the liver transcriptome profile under normal (30 ppt (parts per thousand)), hypo (10 ppt) and hyper (40 ppt) salinity group were compared and analyzed. The results of this study will provide valuable resources for understanding the osmotic regulation process of greater amberjack.