Objective To explore the feasibility and option of different surgeries for neonates with pulmonary atresia and ventricular septal defect (PA/VSD) through assessing the effect of common surgeries. Methods Fourteen neonates who underwent their first surgery in our center from July 2004 to October 2014 were included. Their basic characteristics, operation and pre- and postoperative clinical information were extracted. Follow up was conducted and the last visit was on October 10, 2016. Short- and midterm survival and total correction rate were compared among different surgeries. Results Among the 14 patients, there were 4 (28.6%) patients, 6 (42.9%) and 4 (28.6%) who underwent one-stage repair, right ventricular outflow tract (RVOT) reconstruction, and systemic to PA shunt operation respectively. The overall in-hospital mortality after the first operation was 28.6% (4/14). At last visit, no death occurred resulting the 5-year survival rate of 71.4% (10/14). The overall total correction rate for all neonates was 64.3% (9/14). Although no statistical difference was found in the mortality among the one-stage repair , RVOT reconstruction and systemic to PA shunt group(50.0% vs. 33.3% vs. 0.0%, P=0.280), the survival and hazard analysis implied better outcomes of the systemic to PA shunt palliation operation. There was no statistical difference in the total correction rate and months from the first palliative operation to correction between those who underwent RVOT reconstruction and systemic to PA shunt (75.0% vs. 50.0%, P=0.470; 32.0 months vs. 18.0 months, P=0.400). Conclusion Performing surgeries for neonates with PA/VSD is still a great challenge. However, the midterm survival rate was optimistic for the early survivors. Systematic to PA shunt seemed to be a better choice with lower mortality for the neonates with PA/VSD who need the surgery to survive.