To investigate the effect of low temperature stress on juvenile cobia (Rachycentron canadum), the fish were reared under normal temperature [(30.5 ± 1.0)℃] and low temperature [(20.0 ± 0.5)℃] for 7 days, followed by genome-based transcriptome sequencing of there liver tissues. Each group included 3 biological replicates. The results showed that a total of approximately 243 694 134 raw reads were obtained from the 6 sequencing samples, with Q30 scores exceeding 94% for all samples and GC content raging between 47.65% and 48.16%. A total of 4 362 differentially expressed genes (DEGs) were identified, including 2 793 up-regulated and 1 569 down-regulated genes. KEGG pathway enrichment analysis revealed that in lipid metabolism, a significant number of DEGs were enriched in biological processes such as lipid metabolism, lipid biosynthesis, glycerophospholipid metabolism, phospholipid metabolism and glycerideid metabolism. Key lipid metabolism-related genes, including pparα, pparβ, scd1, cpt1, and cpt2 in the PPAR signaling pathway, played crucial roles in the response of juvenile cobia to low temperature stress. In glucose metabolism, numerous genes were enriched in pathways such as glycolysis/gluconeogenesis, galactose metabolism, starch and sucrose metabolism, and pentose and glucuronate interconversions. Among these, genes such as g6pc and eno were found to play important roles in the adaptation of juvenile cobia to low temperature stress.