INTRODUCTION: Aberrant angiogenesis contributes greatly to endometriosis (EMs) progression, whereas the biological dysfunction of vascular endothelial cells (VECs) in EMs ectopic lesions and the underlying molecular regulatory mechanisms remain largely elusive. METHODS: To uncover the characteristics of VECs and their microenvironment, as well as the key regulatory mechanisms underlying this dysfunctional state in EMs lesions, the proportions of VEC clusters in normal endometrium and EMs lesions were determined by analyzing single-cell RNA sequencing (scRNA-seq) data and verified by immunohistochemistry. The expression levels of VEC markers (such as vWF, CDH5, PECAM-1, and CD34) and genes enriched in angiogenesis-, autophagy-, and cytoskeleton formation-related pathways were analyzed in Gene Expression Omnibus (GEO) datasets. In addition, qRT-PCR, western blotting, autophagy detection, cytoskeleton formation, tube formation, and wound healing assays were performed in vitro. Furthermore, EMs mouse models were established in vivo to verify the pro-angiogenic state of ectopic lesions under high-estrogen and enhanced-autophagy conditions. RESULTS: We found that EMs lesions displayed increased vascular density, aberrant angiogenesis, and a characteristic pro-angiogenic microenvironment. Autophagy levels and cytoskeleton formation in VECs were also significantly increased in EMs. In addition, upregulating autophagy in VECs greatly contributed to accelerated angiogenesis both in vitro and in vivo. Estrogen treatment promoted autophagy in VECs by upregulating estrogen receptor α (ERα) expression. Estrogen-mediated autophagy augmentation also promoted cytoskeleton formation, migration, and tube formation in VECs by downregulating endothelial cell-specific chemotaxis receptor (ECSCR) expression. Moreover, ECSCR expression showed a decreasing trend in EMs VECs compared to VECs in normal endometrium. CONCLUSIONS: In conclusion, high estrogen levels in EMs ectopic lesions contribute to increased autophagy in VECs by upregulating ERα expression. Enhanced autophagy promotes cytoskeleton formation, migration, and tube formation of VECs by downregulating ECSCR expression, thereby contributing to the characteristic pro-angiogenic microenvironment, aberrant angiogenesis in EMs lesions, and disease progression.