Rationale: Abdominal aortic aneurysm (AAA) is a life-threatening cardiovascular disease lacking clinical predictors and effective pharmacologic therapies. The cellular heterogeneity and molecular changes of different cell types during AAA have been revealed in human and mouse aortas by single-cell RNA sequencing (scRNA-seq) technology. However, the heterogeneity and plasticity of endothelial cells (ECs) in AAA remain poorly characterized. Methods: scRNA-seq was performed on the abdominal aorta from angiotensin II (AngⅡ) and salt-induced AAA mice. Additionally, public scRNA-seq data of human and mouse AAA were analyzed with a focus on ECs. Cellular and animal experiments were conducted to validate EC heterogeneity and to investigate the role of SRY (sex-determining region on the Y chromosome)-box transcription factor 18 (Sox18) in endothelial-to-mesenchymal transition (EndMT) during AAA formation. Results: Unbiased clustering analysis identified 20 clusters encompassing 11 cell types. Four subpopulations of ECs were identified in AngⅡ and salt-induced mouse AAA models: Cd36+ lipid-handling ECs, Fn1+ mesenchymal-like ECs, Lrg1+ pleiotropically activated ECs, and Mmrn1+ lymphatic-like ECs. Similar results were observed in human AAA scRNA-seq data. Endothelial dysfunction and EndMT were detected at single cell solution and validated experimentally. Sox18 was identified as a potential EndMT regulator. Sox18 downregulation was confirmed in both human and mouse aortic aneurysm. In vitro, Sox18 siRNA transfection induced EndMT and increased EC permeability via PI3K/Akt signaling pathway. In vivo, EC-specific Sox18 overexpression inhibited EndMT and attenuated AAA formation. Conclusion: Our data reveal the heterogeneity and transcriptional signatures of ECs in AAA at single cell solution, and demonstrate the previously unrecognized role of Sox18-mediated EndMT in AAA, providing novel insights and a promising therapeutic target for AAA intervention.