Background In this study, we aimed to evaluate the association of Vitamin D receptor (VDR) gene polymorphisms with caries risk in children (< 18 years).Methods The electronic databases PubMed, Cochrane, EMBASE, Web of Science, CNKI, Cqvip, and Wanfang were searched for observational studies on the relationship between VDR polymorphisms and caries, including cohort, case-control, and cross-sectional studies. Quality assessment of selected studies was conducted using the Newcastle Ottawa scale. Odds ratios (OR) with 95% confidence intervals (CI) values for associations of individual VDR polymorphisms with dental caries were calculated based on four genetic models: allelic, recessive, dominant, and overdominant. Of 79 studies considered, 10 (nine case-control and one cross-sectional) were selected for analysis; the studies involved seven VDR single nucleotide polymorphisms: rs731236, rs739837, rs10735810, rs2228570, rs7975232, rs1544410, and rs11568820.Results Alleles C and T of rs10735810 were significantly differently distributed in the caries and caries-free groups (OR = 1.33, 95% CI: 1.30–2.30, P = 0.03), with CC + CT genotypes at this locus associated with greater risk of developing caries than the TT genotype (OR = 1.87, 95%CI: 1.15–3.04, P = 0.01). Further, TT + CC genotype at rs731236 was associated with a 1.33-fold higher risk of caries development than the TC genotype (OR = 1.33, 95%CI:1.06–1.67,P = 0.02). On subgroup analysis, the association between rs731236 and caries risk was affected by dentition type, ethnicity, and genotyping method (permanent dentition: OR = 1.48, 95%CI: 1.07–2.03, P = 0.02; Asian: OR = 1.38, 95%CI: 1.02–1.87, P = 0.03; quantitative PCR test: OR = 1.52, 95% CI: 1.10–2.10, P = 0.01). Genotype distributions at rs1544410, rs739837, rs2228570, and rs7975232 did not differ significantly between the caries and caries-free groups.Conclusions Caries risk was associated with rs731236 and rs10735810 genotypes, and rs731236 may be a risk factor for permanent teeth caries among Asian people.