Abstract: We studied the effect of aqueous extract from Huang qi on gene expression profile of doxorubicin induced nephropathy in rats, and explored the molecular mechanism of the intervention. The gene expression profiles of control group, model group and aqueous extract from Huang qi group were detected by using transcriptome sequencing technique. The differentially expressed genes (DEGs) were screened by STEM trend analysis software. GO function enrichment and KEGG pathway analysis were performed for DEGs, and the gene expression level was verified by real-time fluorescence quantitative PCR (RT-qPCR). The results showed that, compared with the control group, 432 DEGs were obtained in doxorubicin nephropathy model group; compared with the model group, 811 DEGs were obtained due to aqueous extract of Huang qi. The results of GO function enrichment and KEGG enrichment analysis indicated that PI3K-AKT pathway (Col6a6, Nr4a1, Sgk1, Gng7) and lipid metabolism-related genes (Cpt1b, Pcsk9, Abca1, Ascm5) were the key pathways and genes in the treatment of doxorubicin induced nephropathy by aqueous extract from Huang qi, which played a protective role in kidney. In conclusion, the molecular mechanism of aqueous extract from Huang qi in protection against doxorubicin induced nephropathy rats is closely related to apoptosis-related genes and lipid metabolism-related genes, suggesting for the need of follow-up study for key gene validation and mechanism of action of aqueous extract from Huang qi for prevention of doxorubicin induced nephropathy.