Subfamily has lived in the anoxic environment of Qinghai-Tibet Plateau for a long time, which is a natural biological model to study the adaptation mechanism of hypoxia. Transcriptome analysis was made on the kidneys of three species of Schizothorax curvilabiatus and Schizothorax macropogon at high altitude （> 3 600 m） and Schizothorax prenanti at low altitude （< 700 m）. By comparing and analyzing the renal transcriptome of Schizothorax unicornis, Schizothorax megacephalus and Schizothorax homostoma, 504 and 478 differentially expressing genes were screened out respectively, among which 199 genes were commonly differentially expressed. The enrichment analysis of common differential genes by GO （Gene Ontology） and KEGG （Kyoto encyclopedia of genes and genomes） showed that the two groups of common differential genes were mainly enriched in glycolysis/glycogen production, lipid biosynthesis, and angiogenesis. Among them, the high expression of eno3, fbp1α, prpf19, and ctsz may play an important role in the long-term adaptation of Schizothorax at high altitude to hypoxic environment. This study provides a new idea for revealing the long-term hypoxia adaptation of plateau fish.