Background: Obesity, especially central obesity, is a risk factor for non-communicable chronic diseases such as dyslipidemia, type 2 diabetes mellitus (T2DM), cardiovascular diseases (CVD), and metabolic syndrome (MetS). Aim: Study the association between the subcutaneous fat area (SFA) and visceral fat area (VFA) with lipid metabolism parameters in adults with MetS. Materials and Methods: Data from 1511 participants who visited the ‘NURA Mongolia’ Ai Health screening center between September 2023 and February 2024, including general information, DEXA (Dual X-ray Absorptiometry), and biochemical analysis results, were used. Metabolic syndrome (MeS) was assessed based on the harmonizing criteria 2009 (≥3 criteria). VFA and SFA were categorized into four groups using quartiles (Q1-Q4). Statistical analysis was performed using SPSS v26, including T-tests, multiple logistic regression (OR, 95% CI), and ROC (AUC) analysis. Results: The average age of the participants was 30.5±3.9 years, with a BMI of 25.1 kg/m², and 49.5% were male. The group with MetS (n=531) had significantly higher levels of VFA and SFA compared to the group that rated their health as relatively healthy and had no clinical diagnosis (n=979) (control group) (p<0.0001), with males showing higher VFA and females showing higher SFA (p<0.0001). The Q4 group for VFA had a significant association with MetS in males (4.611, 95% CI=2.394–9.591) and females (2.253, 95% CI=1.097-3.912) (p<0.001). Logistic regression analysis showed that increased VFA was more strongly associated with MetS in males (β=0.325, p<0.0001) and females (β=0.338, p<0.003) than BMI. The AUC for predicting MetS was 0.790 (95% CI=0.750-0.831) for VFA and 0.401 (95% CI=0.351-0.451) for SFA, with all results being statistically significant (p<0.001). VFA had a higher predictive value compared to other markers. Conclusion In healthy men with metabolic syndrome, VFA is more prominently defined, while SFA is higher in healthy women. Since VFA is a better predictor of metabolic syndrome than SFA, it increases the risk of diseases such as cardiovascular diseases and type 2 diabetes in men, whereas SFA in women serves as a protective factor.