To exhaustively explore the association of infant genetic polymorphisms of methionine synthase (MTR) gene with the risk of non-syndromic congenital heart disease (CHD). A hospital-based case–control study involving 620 CHD cases and 620 health controls was conducted from November 2017 to March 2020. Eighteen SNPs were detected and analyzed. Our date suggested that the genetic polymorphisms ofMTRgene at rs1805087 (GG vs. AA: aOR = 6.85, 95% CI 2.94–15.96; the dominant model: aOR = 1.77, 95% CI 1.35–2.32; the recessive model: aOR = 6.26, 95% CI 2.69–14.54; the addictive model: aOR = 1.81, 95% CI 1.44–2.29) and rs2275565 (GT vs. GG: aOR = 1.52, 95% CI 1.15–1.20; TT vs. GG: aOR = 4.93, 95% CI 1.93–12.58; the dominant model: aOR = 1.66, 95% CI 1.27–2.17; the recessive model: aOR = 4.41, 95% CI 1.73–11.22; the addictive model: aOR = 1.68, 95% CI 1.32–2.13) were significantly associated with the higher risk of CHD. And three haplotypes of G-A-T (involving rs4659724, rs95516 and rs4077829; OR = 5.48, 95% CI 2.58–11.66), G-C-A-T-T-G (involving rs2275565, rs1266164, rs2229276, rs4659743, rs3820571 and rs1050993; OR = 0.78, 95% CI 0.63–0.97) and T-C-A-T-T-G (involving rs2275565, rs1266164, rs2229276, rs4659743, rs3820571 and rs1050993; OR = 1.60, 95% CI 1.26–2.04) were observed to be significantly associated with risk of CHD. Our study found that genetic polymorphisms ofMTRgene at rs1805087 and rs2275565 were significantly associated with higher risk of CHD. Additionally, our study revealed a significant association of three haplotypes with risk of CHD. However, the limitations in this study should be carefully taken into account. In the future, more specific studies in different ethnic populations are required to refine and confirm our findings.Trial registration:Registration number: ChiCTR1800016635; Date of first registration: 14/06/2018.