Background Hexavalent chromium [Cr(VI)] can induce malignant transformation of lung epithelial cells, but its molecular mechanism is still unclear. Objective This study aims to explore the key genes of Cr(VI)-induced malignant transformation of lung epithelial cells and the mechanism of the transformation by bioinformatics analysis. Methods High-throughput gene expression profile data related to Cr(VI)-induced toxic effect was downloaded from the Gene Expression Omnibus(GEO) database, and the co-expressed genes were obtained by the intersection of differentially expressed genes in each dataset. DAVID 6.8 was used to analyze the function enrichment of gene ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathways of the selected differential expression genes. STRING, and Cytoscape 3.8.2 were applied to construct and visualize the protein-protein interaction network. The expressions of Hub genes in lung tumor were obtained by GEPIA2. Results A total of 234 differentially expressed genes were screened out from the GSE24025 and GSE36684 datasets, among which 99 genes were up-regulated while 135 genes were down-regulated. The results of GO and KEGG analyse were mainly concentrated in cell adhesion, negative regulation of cell proliferation, and transcription disorders. A rotein-protein interaction network was generated by STRING database and Cytoscape software. Four functional modules with high scores and 6 Hub genes were finally retrieved. The expression trend of FBLN1 in lung cancer subtypes was consistent with the results of transcriptome screening. Conclusion Cr(VI) exposure causes the differential expression of multiple genes in lung epithelial cells, involving cell morphology, movement, survival fate, phenotype function and signal pathway related to cancer development. FBLN1 may be the critical gene related to malignant cytopathy.