[Objectives] Gymnocypris eckloni, a highly specialized fish species of Schizothoracinae that is endemic to the Qinghai-Tibet Plateau, exhibits remarkable adaptation to extreme high-altitude conditions, including low temperatures and low oxygen. [Methods] To investigate the cold adaptation mechanisms of G. eckloni,this study divided the experimental fish into a control temperature group (14 ~ 16 ℃, indoor recirculating systems, 3 weeks) and a low temperature group (2 ~ 4 ℃, outdoor recirculating systems, 3 weeks). After cold stress, liver tissue samples were collected for histological analysis, expression analysis of genes, and non-targeted metabolomics profiling via liquid chromatography-mass spectrometry (LC-MS). The metabolomic data were processed by principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA). Then, differentially expressed metabolites (DEMs) were identified with criteria of variable importance in projection (VIP) > 1.0, fold change (FC) > 1.5 or FC < 0.667 and P < 0.05. Finally, functional enrichment analysis and integrated analysis of transcriptomic and metabolomic data were conducted. [Results] Although the expression of redox-related genes, sod1, sod2, sod3, and cat, were upregulated, no apparent damage was observed in the liver tissue under cold stress. Metabolomic analysis identified 234 DEMs during cold adaptation, including 138 upregulated and 96 downregulated DEMs (Fig. 6). KEGG pathway analysis showed that the upregulated metabolites were enriched in sphingolipid metabolism (P < 0.05), α-linolenic acid metabolism (P < 0.05), purine metabolism, steroid biosynthesis, cortisol synthesis and secretion, pyruvate metabolism, and glycolysis/gluconeogenesis. The down-regulated DEMs were enriched in histidine metabolism (P < 0.05), linolenic acid metabolism, and arginine and proline metabolism (Fig. 7). Integrated analysis of differentially expressed genes (DEGs) and DEMs showed that the upregulated DEGs and DEMs were enriched in sphingolipid metabolism and pyruvate metabolism, whereas downregulated DEGs and DEMs were enriched in arginine and proline metabolism, histidine metabolism, glutathione metabolism, and valine, leucine, and isoleucine degradation (Fig. 8). Moreover, further DEG-DEM integrated analysis indicated that psat1-L-serine and nr3c1-cortisol maybe as crucial regulators of energy homeostasis, with psat1-serine additionally modulating membrane fluidity—a key adaptation mechanism to cold environments. [Conclusion] G. eckloni undergoes significant metabolic remodeling during cold adaptation, characterized by reduced amino acid metabolism, enhanced lipid metabolism, and increased membrane fluidity. These findings provide insights into the environmental adaptive evolution of plateau fish, providing implications for the conservation of endemic plateau fish species and cold-water aquaculture.