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Background: Metabolic Score for Visceral Fat (METS-VF) is a novel indicator for estimating intra-abdominal fat, yet its connection with coronary artery calcification (CAC) remains uncharted. Our research aims to explore the novel METS-VF indicator’s link to CAC while comparing its performance against relevant anthropometric indices. Methods: This study enrolled participants who underwent health checkups and computed tomography scans for categorizing severity of CAC using the coronary artery calcium score. The METS-VF was calculated and compared with anthropometric indices in estimating the presence of CAC and different CAC severity using receiver operating characteristic curves. Results: Overall, 1217 participants (mean age 50.7 ± 9.9, 53.8% male) were included. METS-VF (odds ratio [OR], 1.506; 95% confidence interval [CI], 1.181–1.921; p = 0.001) was positively associated with the presence of CAC, even after accounting for cardiometabolic factors. Notably, METS-VF was positively associated with mild (OR, 1.450; 95% CI, 1.115–1.886; p = 0.006), moderate (OR, 1.865; 95% CI, 1.137–3.062; p = 0.014), and severe (OR, 2.316; 95% CI, 1.090–4.923; p = 0.029) CAC. Moreover, METS-VF yielded the highest area under curve (AUC) value in the estimation of the CAC presence (AUC = 0.710), mild (AUC = 0.682), moderate (AUC = 0.757), and severe (AUC = 0.807) CAC when compared with body mass index, waist circumference, visceral adiposity index, triglyceride–glucose index, and metabolic score for insulin resistance. The optimal METS-VF cut-off value was 6.4 for predicting CAC. Conclusions: METS-VF emerged as a strong independent marker for detecting CAC presence across mild, moderate, and severe CAC categories, outperforming major anthropometric indices in accurately estimating the presence of CAC and different severity of CAC.