Background Pulmonary atresia with ventricular septal defect (PA-VSD) and major aortopulmonary collateral arteries (MAPCAs) remains a challenging complex congenital heart disease nowadays. In the present study, we aimed to develop a two-stage surgical method and to evaluate outcomes of this method in managing PA-VSD and MAPCAs.Methods Between December 2003 and December 2008, 7 female and 4 male patients between the age of 5 and 10 years who were suffering from PA-VSD and MAPCAs were selected and recruited. The native pulmonary artery trunks were absent in all patients; the lungs were solely supplied by major aortopulmonary collaterals, and the numbers of supplied lung segments ranged from 15 to 20 (17.9±1.6). There were a total of 43 MAPCAs in all the patients (3-5 (3.9±0.7) MAPCAs per patient). The accumulated Nakata index was (222.9±29.9) mm~2/m~2 (ranged from 182 to 272). All the patients underwent two sequential operations. Stage one included left major aortopulmonary collateral unifocalization and modified Blalock-Taussig shunt from left posterior lateral thoracotomy; stage two comprised right unifocalization, ligation of the shunt, followed by ventricular septal defect closure and right ventricular outflow tract reconstruction assisted with cardiopulmonary bypass from midline stemotomy.Results All the patients survived the initial surgery, but one of them died of low cardiac output syndrome on the third day after the second operation. Postoperative complications included pneumonia in one case and capillary leak syndrome in another. Postoperative oxygen saturation maintained about 95%-100%, which was significantly higher than pre-operation (P <0.01). During the follow-up period of 3-51 (25.4±15.2) months, there were no late death and no need for re-intervention. All the patients enjoyed their lives with good conditions.Conclusions This two-stage complete repair strategy was well-tolerated and effective with good outcome, thus offering an altative surgical approach in the treatment of PA-VSD and MAPCAs.