To reveal the association between DNMT1 polymorphisms and congenital heart disease (CHD) in child patients, a total of 224 CHD child patients as well as 199 healthy individuals were enrolled in the present study. The DNA was extracted from whole blood, and four SNPs including rs16999593, rs2228612, rs2288349 and rs10420321 were selected for the gene polymorphism investigation via ligase detection reaction (LDR) assay. Odds ratios (ORs) and 95 % confidence intervals (95 % CIs) were used to assess the strength of the association. rs16999593 was associated with the CHD under the heterozygous (CT vs TT: OR 0.62; 95 % CI 0.41–0.95; p = 0.03), dominant (CT + CC vs TT: OR 0.63; 95 % CI 0.42–0.95; p = 0.03), and allele models (C vs T: OR 0.07; 95 % CI 0.50–1.00; p = 0.05). rs2228612 was related with the CHD under the heterozygous (AG vs AA: OR 0.42; 95 % CI 0.27–0.65; p = 0.0001), homozygous (GG vs AA: OR 0.43; 95 % CI 0.240–0.77; p = 0.004), dominant (AG + GG vs AA: OR 0.42; 95 % CI 0.28–0.64; p < 0.0001), and allele models (G vs A: OR 0.62; 95 % CI 0.47–0.82; p = 0.0007). rs10420321 correlated with the CHD only under the recessive model (GG vs AG + AA: OR 0.61; 95 % CI 0.37–1.01, p = 0.05). However, no significant association between the rs2288349 polymorphisms and the risk of CHD was observed (p > 0.05). DNMT1 polymorphisms might contribute to the risk of CHD, especially rs16999593 and rs2228612.