Background: This paper aimed to study the association of serum Vitamin D level and Body Mass Index (BMI) as representatives of malnutrition at micro and macro levels, respectively, on dental caries. Method and Participants: A total of 333 randomly selected children aged 6–12 years in Sulaimani, Kurdistan, Iraq were examined for three variables of the Decayed Missed Filled Tooth (DMFT) index, BMI, and Vitamin D serum levels in a single-time cross-sectional snapshot. Results: The majority of the population studied (70%) were Vitamin D deficient. In the linear regression analysis, both Vitamin D and BMI had insignificant effects on DMFT, withp-values of 0.22 and 0.55, respectively. After the categorization of the data, the risk estimate between normal (≥20 ng/mL) and deficient (<20 ng/mL) Vitamin D groups with regards to the caries and caries-free categories was 1.97 (95% CI: 0.91–4.24). According to the mean and median of the DMFT, which were both 4, the sample is categorized into the low-caries group (DMFT < 4) and high-caries group (DMFT > 4). When these groups are compared to Vitamin D levels and taking 20 and 15 as thresholds, the odds ratios were 1.19 (CI: 0.74–1.92) and 1.88 (CI: 1.20–2.94), respectively. Regarding the BMI, a normal BMI increases the chances of having a lower caries index (OR = 1.83, CI: 1.10–3.03). Conclusions: Our results show that having a serum Vitamin D level ≥15 ng/mL and having a normal BMI are associated with a lower caries index in children.