Abstract: Objective To investigate the polymorphism of folate metabolism pathway genes in pregnant women with congenital heart diseases(CHD), and to explore the relationship between the gene polymorphisms and the susceptibility to CHD. Methods According to the inclusion criteria, Collected 320 cases of fetal congenital heart disease diagnosed by color Doppler echocardiography. From peripheral venous blood, PCR-RELP method was used to detect the polymorphism of MTHFR677 and MTHFR1298 loci. Results ①Gene loci polymorphism:In the control group and CHD group, C and T allele、A and C alleles all have differences in the 2 groups was statistically significant(χ²=16.589, P<0.001; χ²=5.078, P=0.020); ②Genotype polymorphism:In the control group and CHD group, CC, CT, TT genotype have differences in the both groups was statistically significant(χ²=15.282, P<0.001). AA, AC and CC genotype have no statistically significant difference in 2 groups(χ²=5.092, P=0.080); ③In the study of stratified:Tetralogy of fallot group CC, CT and TT genotype and AA, AC and CC genotype, with the control group there were statistical significance (χ²=7.794, P=0.020; χ²=8.998, P=0.010); Ventricular septal defect group CC, CT, TT genotype, with the control group there were statistical significance(χ²=10.407, P<0.001), And AA, AC and CC genotype, with the control group there were no statistical significance(χ²=0.667, P=0.720). Conclusion The MTHFR C677T polymorphism of mother is associated with congenital heart disease in children. Hierarchical research tips that the MTHFR C677T polymorphism of mother is associated with occurrence of tetra logy of fallot and ventricular septal defect in children. The other results in the case group and the control group MTHFR A1298C genotype although no obvious difference, but the A/C allele is having the significant difference, prompt allele A/C to children is A risk factor of CHD.