Objective To summarize the experience of the surgical treatment of complex congenital heart diseases in 29 newborns. Methods Twenty-nine newborns were operated on for various congenital heart diseases, ages were from 3 to 28 d. There were ventricular septal defect 3 cases, D-transposition of the great arteries (D-TGA) 10 cases, pulmonary atresia (PA) 1 case,tricuspid atresia 3 cases, single ventricle 1 case, tetralogy of Fallot 6 cases, endocardial cushion defect 4 cases and truncus arteriosus 1 case. All patients were combined with atrial septal defect and patent ductus arteriosus. All operations were performed under hypothermic cardiopulmonary bypass. Results The operative mortality was 13.8%(4/29). One case with D-TGA and 1 case with PA succumbed due to low cardiac output syndrome, and 2 cases due to acute respiratory distress syndrome and low blood oxygen saturation. Twenty-five cases were discharged. Follow-up was completed in 19 patients,with a duration of 1-31 months, all patients have been normal. Conclusion Anesthesia and cardiopulmonary bypass should be performed smoothly and satisfactorily in newborn babies for cardiac surgery. Surgical manipulation should be accurate with less trauma and well protection of myocardium and lung is important.