Purpose Prenatal diagnosis of congenital heart disease, backed by its recently improved accuracy, has become widespread; however, prenatal diagnosis must be accompanied by multidisciplinary counselling in order to ensure proper management of congenital heart disease and reduce the rate of abortion. This study aims to evaluate the efficacy of multidisciplinary prenatal counselling for parents on the rate of abortion and the surgical outcomes of congenital heart disease patients. Methods We studied 273 patients who were referred to cardiothoracic surgery for prenatal counselling of congenital heart disease from May 2007 to April 2017. All patients were referred from obstetrics department to cardiothoracic surgery department. We retrospectively reviewed the patients’ medical records. We compared our data and that of another paper published in 2006. The latter was a result of our hospital before we began prenatal counselling in 2007; the data ranges between July 1988 and June 2003. In comparing the two data sets, we tried to quantify the efficacy of prenatal counselling. Results A total of 307 pregnancies diagnosed as congenital heart disease were referred to cardiothoracic surgery department; medical records were available in 273 cases (88.9%). In this study, the mean gestation age at diagnosis was 28±5.2 weeks. The mean maternal age was 35±4.1 years old. Abortion rate was 1.5% (4/273). The incidence of associated extracardiac anomalies and chromosomal abnormalities was 19.8% (54/273) and 5.5% (15/273), respectively. Overall agreement of screening ultrasonography and prenatal echocardiography was 77.7%. The overall survival rate of fetus was 82.8% (226/273). No difference was found in disease severity and maternal age between delivery group and abortion group ( P=0.077). Operative mortality was 7.9% (16/227). Conclusions Prenatal multidisciplinary counselling is effective for lowering the abortion rate and increasing the proportional birth rate of complex heart disease patients in regard to those with simple heart disease. In addition, prenatal counselling offers good rapport between the medical team and the patient, and improves the clinical outcomes of complex heart disease patients after birth.