Objective The study was conducted to identify the risk factors of congenital heart disease(CHD) in Zhoushan Archipelagoes, providing evidence for the development of corresponding preventive strategies. Methods The nested case control study was population based and retrospective, with 45 CHD patients recruited according to the data from the birth defect surveillance database in Zhoushan from 2000 to 2006, and 135 randomized control subjects collected, the ratio of frequency being 1∶3. Results According to the results of multivariate logistic regressions, the paternal age, oral contraceptives used within 6 months before pregnancy, and maternal syphilis infections were considered influential variables.Compared with the younger group (with the paternal age 25), pregnant women who had 26 to 30 year old spouses presented significantly higher risks to have CHD fetuses, the OR being 9.61 (95% CI: 1.17-78.94), whereas no distinguishable difference was shown when comparing to the 31 year old group. Exposure to contraceptives or syphilis infections within 6 months before pregnancy also added to the risks, the OR being 5.48 (95%CI：1.48-20.30) and 4.36 (95%CI：1.26-15.05), respectively.Conclusion Exposure to contraceptives or syphilis infections within 6 months before pregnancy would add to the risks of having fetuses with congenital heart diseases. Therefore, preventive intervention shall be given.