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Abstract Background Information on the distribution of Metabolic syndrome (MetS) and its combinations by urban/rural areas in lower-middle income countries has been limited. It is not clear how the various combinations of MetS components varied by urban/rural population and if particular combinations of MetS are more common. This study aimed to estimate the prevalence of MetS and combinations of MetS components according to sex and urban/rural areas from a nationally representative sample of Thai adults. Methods Data from the fourth National Health Examination Survey of 19,256 Thai adults aged 20 years and over were analyzed. MetS was defined using the harmonized criteria of six international expert groups with Asian-specific cut-point for waist circumference. Results The prevalence of MetS was 23.2% among adults aged ≥ 20 years (19.5% in men and 26.8% in women). Among men, the prevalence of MetS in urban was higher than those in rural areas (23.1% vs 17.9%, P < 0.05), but among women, the prevalence was higher in rural areas (27.9% vs 24.5%, P < 0.05). Overall, an individual component of low high density lipoprotein (HDL) and hypertriglyceridemia were more common in rural areas, while obesity, high blood pressure and hyperglycemia were more common in urban areas. The most common combination of MetS components in men was the clustering of low HDL, hypertriglyceridemia, and high blood pressure (urban: 3.4% vs. rural: 3.9%, adjusted OR 0.9, 95%CI 0.7, 1.1). Among women, the most common combination was the clustering of obesity, low HDL, and hypertriglyceridemia (urban: 3.9% vs rural: 5.9%, adjusted OR 0.8, 95%CI 0.6, 0.9), followed by the clustering of these three components with high blood pressure (urban: 3.1% vs. rural 4.5%, adjusted OR 0.8, 95%CI 0.7, 0.9). Conclusion Metabolic syndrome affects both urban and rural population with different pattern of MetS combinations. Dyslipidemia and obesity were the most common components among women in rural areas, hence, interventions to prevent and control these factors should be strengthened.