Objective To investigate the long-term effects and mechanism of endometriosis (EMT) on subclinical cerebrovascular disease and cognitive function by comparing the postmenopausal women with physician-diagnosed endometriosis and those without. Methods From May 2018 to August 2020,154 outpatients and inpatients in the Department of Obstetrics and Gynecology in the General Hospital of Eastern Theater Command were selected. According to the history of endometriosis, postmenopausal women were divided into EMT group (77) and control group (77). Magnetic resonance angiogram (MRA) were performed on the brain to assess cerebral white matter lesion (WML), lacunar infarct (LI) and intracranial artery stenosis. The carotid artery plaque was measured by carotid duplex scans. Cognitive functions were evaluated in both groups. SPSS statistics 22.0 was used for data analysis, χ² test or paired t test for intergroup comparison. Logistic regression was performed to analyze the risk factors of neck arterial plaques and WML. Results The EMT group had more WMLs [40.3%(31/77) vs 22.1%(17/77)] and carotid artery plaques [36.4 %(28/77) vs 19.5%(15/77)] than the control group (P<0.05). In the logistic regression models, endometriosis was an risk factor for WML (OR=3.041,95%CI 1.405-6.586) and carotid artery plaque (OR= 2.971,95%CI 1.340-6.483) after adjusting for age, hypertension and dyslipidemia (P<0.05). The EMT group scored lower than the control women in tests of word learning, symbol digit substitution, animal category fluency (P<0.05). Conclusion EMT is a risk factor for WML and carotid plaques and has a long-term impact on subclinical cerebrovascular diseases and cognitive functions in the postmenopausal women.