Background: Atherosclerosis (AS) is a chronic inflammatory disease characterized by plaque formation and endothelial dysfunction. Under pro-inflammatory conditions, the endothelial-mesenchymal transition (EndMT) plays an important role in the pathogenesis of AS. Resveratrol (RES) is a natural polyphenol in traditional Chinese medicines, which has been proven to possess anti-AS effects. However, the mechanism of RES treating AS through EndMT is not clear at present. Methods: RES targets were screened using databases such as SwissTargetPrediction and TargetNet, and AS and EndMT targets were searched using databases such as OMIM and DisGeNET. With the help of Venny 2.1, the key targets were selected by intersection. Next, the protein-protein interaction (PPI) network was constructed through the STRING 11.0 platform and Cytoscape software; gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotations were performed using DAVID. Further, Cytoscape was used to construct a drug-component-gene target-pathway network diagram to identify the core components and genes. Subsequently, an AS rat model was established. The blood lipid level of rats was detected by an automatic biochemical analyzer, and the expression level of the target protein was measured by western blotting. Results: Through network pharmacology analysis, 37 potential targets for RES treating AS and EndMT were identified, and the core targets for RES treating AS consisted of AKT1, TNF, MIMP9, and PPARG. GO enrichment analysis indicated that the treatment of AS with RES mainly involved the migration and proliferation of epithelial and endothelial cells. The KEGG pathway enrichment analysis revealed that the enrichment of TNF and Rap1 signaling pathways was most significant. Besides, RES effectively reduced the levels of total cholesterol (TC), triglyceride (TG) and low-density lipoprotein cholesterol (LDL-C) in the serum of AS rats, increased the level of high-density lipoprotein cholesterol (HDL-C), and significantly cut down the atherosclerosis index (AI). Twist1, calponin, α-SMA and VE-cadherin were considered as EndMT indexes. The results of the western blot demonstrated that the protein levels of Twist1, calponin and α-SMA were significantly decreased, while the protein expression level of VE-cadherin was notably increased in rats treated with RES. Moreover, RES could also reduce the expression levels of Rap1 and Epac1 proteins. Conclusion: RES is an effective anti-AS drug. Briefly, RES can effectively improve the blood lipid level of AS patients, regulate the expression of EndMT-related proteins, and alleviate the dysfunction of endothelial cells. Notably, the functions of RES are closely associated with the EPAC1-Rap1 pathway.