Objective To investigate the molecular mechanisms of gene expression and response in mouse kidney tissue during adaptation to hypoxic stress in the plateau based on transcriptome sequencing technology. Methods In this study, C57BL/6 mice were reared at 4200m (high altitude kidney test group, HKT) and 400m (plain kidney control group, PKC) above sea level, and kidney tissues were removed aseptically after 30 days for transcriptome sequencing using high-throughput RNA-sequencing (RNA-Seq) was used to sequence the transcriptome. The sequencing results from the HKT and PKC groups were analyzed by gene ontology (GO) annotation and enrichment in the Kyoto encyclopedia of genes and genomes (KEGG), and the reliability of the sequencing results was verified by quantitative reverse transcription?PCR (RT-qPCR). Results Compared to the PKC group, 1349 differential genes expression was upregulated（p<0.05）and 1658 differential genes expression was downregulated in the HKT group（p<0.05）. Among them, prolactin receptors(PRLR), apolipoprotein E(APOE), apolipoprotein A4(APOA4), cytochrome c somatic(CYCS), acyl-Coenzyme A oxidase 1(ACOX2), cytochrome c oxidase subunit 5A(COX5A), cytochrome c oxidase subunit 5B(COX5B), cytochrome c oxidase subunit 7A(COX7) and heat shock protein β-1(HSPB1) genes were significantly enriched. GO annotation analysis and KEGG enrichment analysis showed that differential genes were significantly enriched in organelle inner membrane, mitochondrial inner membrane and mitochondrial protein complexes, in addition to peroxisomal, oxidative phosphorylation, thermogenesis, carbon metabolism and tricarboxylic acid cycle pathways. Conclusion Hypoxic stimulation at high altitude may cause oxidative stress, inflammatory response and imbalance of lipid metabolism in the body by affecting energy metabolism-related pathways in vivo.