This study aims to identify the regional distribution in the prevalence of dental caries and related multidimensional factors among 12-year-old children in Korea. Data from the 2018 Child Oral Health Survey were used to calculate the average DMFT index of 12-year-old children in metropolitan cities, and a multi-level regression model was applied to explain the regional distribution of dental caries prevalence and related factors. Factors were divided into two levels by administrative structure. This study finds a significant regional difference in the prevalence of dental caries in 12-year-old Korean children across metropolitan cities. Multilevel analysis showed that districtlevel factors (average number of pit and fissure-sealed permanent teeth, dental treatment demand rate, preventive treatment rate, sex ratio, and number of dentists per 100,000 people) and metropolitan-level factors (intakes of cariogenic beverages and number of pediatric dental hospitals and clinics per 100,000 people) had a significant effect on dental caries prevalence (<i>p</i> < 0.05). Individual characteristics and local socio-environmental factors influence the prevalence of dental caries. Especially considering the strong dependence on preventive treatment and accessibility to dental care services, it is necessary to provide adequate preventive treatment and expand health care resources in high-risk areas of dental caries.