Abstract: Objective Based upon the bioinformatic analysis of gene chip data between patients with diabetic kidney disease(DKD)and normal controls, differentially expressed genes of epithelial mesenchymal transformation of DKD were screened for elucidating its pathogenesis and predicting the potential therapeutic Chinese medicine for DKD. Methods GSE23338 microarray data were downloaded from gene expression omnibus, related differentially expressed genes screened by R language and differentially expressed genes analyzed by Gene Ontology, Kyoto Encyclopedia of Genes and Genomes. Through the analysis of STRING website for establishing a network of protein-protein interaction(PPI)and Cytoscape software and its plug-ins for obtaining key core genes, core genes were mapped to Coremine Medical for screening the relevant therapeutic Chinese medicines for DKD. Results A total of 187 differential genes were screened, including 94 up-regulated and 93 down-regulated genes. Pathway enrichment results included the signaling pathways of tumor necrosis factor, TGF-β and AGE-RAGE. And key core genes included FN1, TGFB1, COL1A1, SERPINE1, SNAI2, THBS1, MMP1, CDH2, JAG1 and VCAM1. The selected TCM herbs included astragalus membranaceus, plantain, centella, coptis chinensis, scutellaria baicalensis and panax notoginseng. Conclusion Analysis of differentially expressed genes and key core genes promotes understanding of the pathogenesis of DKD and provides probable gene targets and research rationales for developing new drugs of DKD in traditional Chinese medicine.