Abstract: Objective To summarize the clinical experience for complex congenital heart disease treated with modified Fontan operation. Methods From November 1996 to May 2005,124 patients (male 83,female 41; including tricuspid atresia, single ventricle, double outlet of right ventricle, malposition of great arteries, pulmonary atresia, corrected transposition of great arteries, hypoplastic rightheart syndrome, etc.) underwent modified Fontan operation at age 7.6±5.5 years. Noncardiopulmonary bypass was used in 19 patients, 105 patients with cardiopulmonary bypass. Right atria-pulmonary artery connection were performed in 17 patients, right atria-ventricular connection were performed in 19 patients, and total cavopulmonary connection (TCPC) were performed in 88 patients. Staged operation were performed in 23 patients. Results The hospital mortality (30 days postoperative) was 13.7% (17/124). The hospital mortality of patients undergone right atria-pulmonary artery connection was 23.5%(4/17), patients undergone right atria-ventricular connection was 15.8%(3/19), patients undergone TCPC was 11.4%(10/88), patients undergone operation with fenestration was 14.6%(6/41), and the patients undergone staged operation was 8.7%(2/23). Low cardiac output syndrome, multiple organ failure, and ventricular fibrillation were the cause of death. Morbidity of complications was 16.9％(21/124) in early period. Complications consisted of pleural effusion, arrhythmia, pericardial effusion and low cardiac output syndrome, etc. Eightynine patients were followed up, followup time was from postoperative 6 months to 65 months. Re-hospitalization rate was 6.5%, and re-operation rate was 0.9%. There were pleural effusion in 3 patients, pericardial effusion in 3 patients, and obstruction of inferior vena cava in 1 patient. All patients recovered. Conclusion Modified Fontan operation is an optimal procedure for functional single ventricle, fenestration seems to decrease postoperative pleural effusions.