Abstract: The extreme environmental features of low temperature and low oxygen on the Qinghai-Tibet Plateau provide a natural laboratory for the evolution of biological adaptability. The subfamily Schizothoracinae are widely distributed in the water bodies surrounding the Qinghai-Tibet Plateau, and has adapted to the unique highland environment through long-term evolutionary process. In this study, we focused on two high-altitude (>3 000 m) Schizothoracinae fish species (Schizothorax macropogon and S. waltoni) and one low-altitude (<1 000 m) ancestral Schizothoracinae fish species (S. prenanti) to conduct a transcriptome sequencing comparative analysis regarding the liver tissues, which is the main energy metabolism organ in fish species. This analysis reveals the key signaling pathways involved in the adaptation of highland Schizothoracinae to high-altitude environment. Comparing the liver transcriptomes of high-altitude with those of low-altitude Schizothoracinae, we identified 106 genes that shared differential changes in expression between the two high-altitude species. Among these genes, 66 were upregulated and 40 were downregulated. GO and KEGG enrichment analysis reveals that the most important pathways for high-altitude adaptation in Schizothoracinae include oxidation-reduction processes, pathways related to blood development, amino acid metabolism and steroid biosynthesis. Among them, genes related to oxidation-reduction and blood development (faxdc2, cpox, cyp51, and NADH-cytochrome b5 reductase 2) with high expression levels might play a crucial role in high-altitude adaptation. The study provides new insights into the molecular mechanisms underlying the adaptation of fish to high-altitude environment.