Abstract: Objective To analyze gene-environment interactive effects on congenital heart disease(CHD) with crossover analysis and to provide a new method for etiological research of CHD.Methods Using hospital-based case-control design and questionaire survey,137 mothers of children with CHD and 132 of children with diseases other than CHD or congenital malformation hospitalized in department of thoracic surgery in four hospitals during the period of July 2012 through October 2013 were investigated.The fasting peripheral venous blood samples of the children were collected for DNA extraction and gene detection.Crossover analysis was adopted to assess interactive effects of CHD gene(MTHFR C677T mutation)and environment(pregnant morbidity of the mothers).Results There were significant differences in the percentages of genotypes of CC(20.44%vs.36.36%),CT(38.69%vs.40.91%),and TT(40.87%vs.22.73%) and of allees of C(39.78%vs.57.58%)and T(60.22%vs.42.42%)between the cases and the controls(P <0.010 for all).Crossover analysis showed that there was a statistically significant interaction between CHD pathogenic MTHFR gene C677T mutation and environmental factors(maternal morbidity) based on the additive model(U=2.060,P=0.020),with the evaluation indexes of synergy index(SI) of 4.85,attributable proportion(AP) of 70%,AP^* of 79%,and relative excess risk due to interaction(RERI) of 5.64.But no significant interaction was observed based on the results of multiplicative model(P >0.05).Conclusion There is an additive interaction between CHD MTHFR C677T gene mutation and maternal morbidity for incidence of CHD.