Objective To investigate the environmental risk factors associated with the development of congenital heart diseases (CHD). Methods Eighty-six children with CHD were screened from 16 698 children aged between 0 to 5 years in Bengbu, Anhui Province by stratified cluster sampling. A population-based 1∶1 matched case-control study was conducted, and each case was matched with one normal control by gender and birth date (with difference no more than one month). The risk factors of CHD were analysed by univariate and multivariate Logistic regression analysis. Results Four risk factors were screened to be associated with the development of CHD, including maternal exposure to poisonous chemicals during first trimester of pregnancy (OR, 1.745), maternal respiratory infection during first trimester of pregnancy (OR, 1.747), abnormal childbearing history（OR, 1.644）and river around the dwelling place（OR, 1.487）. Conclusion Maternal exposure to poisonous chemicals and maternal respiratory infection during first trimester of pregnancy, as well as abnormal childbearing history and river around dwelling place are major environmental risk factors contributing to CHD in neonates.