Abstract: Salinity is an important environmental factor that affects the life cycle of aquatic organisms, including their growth, development and reproduction. In fish, acute salinity changes cause a series of physiological responses. Hippocampus kuda is an important economic resource and can adapt to a wide range of salinity levels, while the juveniles are highly sensitive to salinity stress, which may cause pathological signs or diseases by alleviating the immune roles and then lead to mass mortality. The survival rate of cultivated H. kuda is low in China because of the toxic effects of salinity stress on juvenile seahorse. To understand molecular mechanisms of its low survival rate, this study used high-throughput sequencing technology to analyze differentially expressed genes (DEGs) in juvenile seahorse hepatopancreatic tissues treated with normal-salinity water (CK, salinity=25‰), low-salinity water (LS-test, salinity=17‰), and high-salinity water (HS-test, salinity=31‰) respectively for 12h. According to the result of RNA-Seq, a total of 71794 unigenes were produced among control group, high-salinity stress group and low-salinity stress group, and the sequence N50 value was 1780 bp, with an average length of 820.71 bp. Compared with the control group, there were 2740 differently expressed genes selected in high salinity group, of which 495 genes were up-regulated and 2245 were down-regulated. On the other hand, 3715 differently expressed genes were selected in low-salinity group, of which 1854 genes were up-regulated and 1861 genes were down-regulated. Ten dysregulated DEGs (Gst, Bcl-2, Fas, Vlcad, Pdha1, Mdh1, Idh3b, G6pd, Gadd45α and SOD) were confirmed by qRT-PCR. According to the result of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the DEGs were mainly related to metabolism and immune responses. With respect to metabolism, the low-salinity group had enhanced energy and amino acid metabolism, while high-salinity group had reduced lipid metabolism related genes expression. Both high- and low-salinity group had enhanced immune metabolism pathways. Based on our results, we collected the lipid metabolism related genes (Fadsd6, Fas, Sqle, Cyp51, Elovl6 and Slc27a6), amino acid metabolism related genes (Gldc, Atp6v1e1, Sms, Fadh, Asl, Ass1 and Glud1), energy metabolism related genes (Vlcad, Pdha1, Mdh1, Idh3b, G6pd and Sdhd) and immune related genes (Gst, Hsp70, Hsp90, Sod, Bcl-2, Gadd45α, Tcrβ, Tap2 and Traf3) of H. kuda as genetic indicators to identify the stressor. This study will promote the discovery of the molecular mechanism of salt stress adaptation of aquatic organisms, and provides a reference for ambient salinity control in aquaculture.