Purpose Middle-aged women often experience weight gain, particularly as visceral fat, due to hormonal changes associated with menopause. Visceral fat, which accumulates in the abdomen, poses significant risks to cardiometabolic health. This cross-sectional study aimed to compare the cardiometabolic risks associated with Visceral Fat Obesity (VFO) and Subcutaneous Fat Obesity (SFO) in middle-aged Korean women and to identify factors that influence VFO. Methods Women aged 40 to 64 with overweight or obesity were recruited from March to April 2019. The study involved anthropometric measurements, fasting blood tests, and low-volume abdominal computed tomography. Additionally, participants provided self-reported sociodemographic, health-related, and lifestyle information, including Physical Activity (PA) and dietary intake. Results Of all participants, 70.8% were post-menopausal, and 55.1% had VFO. Those with VFO exhibited significantly higher mean values for waist circumference, total cholesterol, low-density lipoprotein cholesterol, triglycerides, fasting glucose, high sensitivity C-reactive protein, and the Framingham risk score compared to those with SFO. The factors influencing VFO were age (odds ratio (OR)=1.14; 95% confidence interval (CI), 1.032~1.247), body mass index (OR=1.47; 95% CI, 1.151 ~1.875), days of vigorous PA per week (OR=0.42; 95% CI, 0.244~0.735), and intake of animal calcium (OR=0.99; 95% CI, 0.988~0.997). Conclusion The findings indicate that middle-aged women with VFO face increased cardiometabolic risks. Since menopause is inevitable in women, targeting modifiable behaviors to reduce weight, particularly visceral fat, is crucial for lowering cardiometabolic risk.