Abstract: This study aims to explore the molecular mechanism of the effect of fibroblast growth factor 13 on the occurrence and development of non-small cell lung cancer. A lung cancer cell line A549 with FGF13 knock-down was obtained by constructing eukaryotic expression vector interfering with FGF13 and packaging with lentivirus. RNA Sequencing（RNA-seq） was used to detect gene expression profile and screen differentially expressed genes. The differentially expressed genes were enriched and analyzed by GO and KEGG to verify the expression level of some DEGs. The key genes in the protein-protein interaction（PPI） network encoded by DEGs were screened by STRING online database, and the prognosis of key genes was analyzed by UALCAN database. Compared with the control group, a total of 1 114 DEGs were screened in lung cancer cell line A549 with FGF13 knock-down（P≤0.05, difference multiple≥2）, of which 672 and 442 DEGs were up-regulated and down-regulated respectively. Six genes including CXCL10 and SELE were verified by real-time quantitative PCR（RT-qPCR）, and the results were consistent with the results of sequencing. GO enrichment analysis showed that DEGs was related to biological processes such as apoptosis, cell migration and redox. KEGG enrichment analysis showed that DEGs was related to p53 signal pathway, TNF signal pathway, PI3 K-AKT signal pathway and so on. In the interaction network of DEGs-encoded proteins, CXCL10, CCL5, IL6, DDX58, BST2, CSF2, CCL4, IFIH1, CMPK2 and CXCL1 were potentially key genes regulated by FGF13, among which DDX58 and IFIH1 were significantly related to the prognosis of patients. In this study, transcriptome sequencing analysis revealed the DEGs regulated by FGF13 in lung cancer A549 cells and its related signal pathways and biological processes, which provided a scientific basis for the follow up study of the biological function and molecular mechanism of FGF13 in lung cancer cells.