Background <p>Previous studies have suggested the close link between endometriosis and body size index. However, there are inconsistent associations between central, general, and visceral adiposity index and endometriosis. This study aimed to evaluate and compare trend of general, central, and visceral adiposity indices in women with and without endometriosis using longitudinal population-based data.</p> Methods <p>We analyzed data from 3159 premenopausal women aged 20–45 years with defined status of endometriosis who participated in the TLGS from phases 3 to 7. The interval between phases was 3 years. Adiposity indices including general (body mass index), abdominal (waist circumference, waist-to-hip ratio, waist-to-height ratio) and visceral (lipid accumulation product, a body shape index, body roundness index, and visceral adiposity index) were evaluated. Generalized Estimating Equations were used to examine longitudinal trends and associations of endometriosis status with adiposity indices, adjusting for age, parity, smoking, education, and physical activity.</p> Results <p>Among the participants, 421 women (13.3%) had diagnosed endometriosis. All adiposity indices showed significant increasing trends over time in both groups. Endometriosis status was not significantly associated with general or central adiposity indices. However, among visceral adiposity measures, the visceral adiposity index was consistently higher in women with endometriosis (adjusted difference: 0.56; 95% CI: 0.10–1.03; <i>p</i> = 0.016), indicating greater visceral fat accumulation.</p> Conclusions <p>This study is the first to use longitudinal population-based data to simultaneously evaluate general, central, and visceral adiposity indices in women with endometriosis. Findings indicate that visceral adiposity, rather than general or central obesity, may represent a metabolically relevant phenotype.</p>