To investigate the relationship between Heart Rate Variability and menopause among obese middle-aged women in Korea. Subjects and Methods Forty middle-aged women (age 49.05 ± 2.64 years) with BMI > 23㎏/㎡ were recruited by local advertisement. Blood profiles of estrogen, FSH, LH, glucose, total cholesterol, HDL-cholesterol, and triglyceride were measured. Autonomic Nervous System (ANS) was estimated by short-term spectral analysis of heart rate variability (HRV). Visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) were accessed using Computerized Tomography (CT), Bioimpedance Analysis (BIA), and anthropometry. To scrutinize the influence of ANS on obesity-related factors, we divided the subjects into pre- and post-menopausal women. Results The total cholesterol, FSH and LH were significantly higher in post-menopausal obese women group. The estradiol and standard deviation of all normal R-R intervals (SDNN), high-frequency components (HF) of the HRV were significantly lower in postmenopausal obese women group (P<0.05). Adipose tissue distribution and blood profiles were not significantly different between two groups. Conclusion Menopause induced a decrease in SDNN and HF values and increase in total cholesterol level in obese women although the VAT itself was not related with ANS in obese women.