Dental caries is a multifactorial disease and the cause of caries has been studied for many years. Herein, a meta-analysis purposed to estimate the association between polymorphism of Carbonic anhydrase VI (CA VI), Ameloblastin (AMBN), and Toftelin (TUFT1) genes and dental caries susceptibility. Four databases of Cochrane Library, Web of Science, PubMed/Medline, and Scopus databases were searched comprehensively until February 13, 2020. The pooled analyses were implemented by Review Manager 5.3 software and publication bias analyzed by the Comprehensive Meta-Analysis version 2.0 software. Eight studies were included and analyzed in the meta-analysis. The pooled analyses illustrated that the CA VI rs2274328, CA VI rs2274333, CA VI rs2274327, AMBN rs4694075, AMBN rs34538475, TUFT1 rs4970957, and TUFT1 rs3790506 polymorphisms were not associated with the susceptibility to dental caries. The age group and ethnicity were not effective factors on the results of the polymorphisms. The sensitivity analyses confirmed the stability of the pooled results. In addition, there was no publication bias across the studies. The results of this meta-analysis suggested a lack of association between AMBN, TUFT1, and CA VI polymorphisms and susceptibility to dental caries.