Abstract: Objective To explore the impact of prenatal diagnosis on the early treatment and short and medium term outcome of neonatal pulmonary atresia with intact ventricle septum (PA/IVS) or critical pulmonary stenosis with intact ventricle septum (CPS/IVS). Methods According to the case-control method, twenty-eight neonates with (PA/IVS) or (CPS/IVS) who had percutaneous pulmonary balloon valvuloplasty (PBPV) surgery indications, were divided into the prenatal diagnosis group (n = 15) and the postnatal diagnosis group (n = 13). The prenatal diagnosis group was diagnosed in fetal period and the intervention program was since developed . The postnatal diagnosis group was referred from other hospitals, and the intervention program was developed after confirmation of the diagnosis. All the neonates accepted the PBPV surgery after the hemodynamic parameters stable. All neonates were followed-up at 1 month, 3 months, 6 months, 1 year, and 2 years after surgery. Clinical situations, echocardiography results, and interventional cardiology measurements were compared between two groups. Result The average age and weigh was 7.53 ± 3.18 days and 3102.32 ± 708.40 g respectively at the time of PBPV surgery in 28 neonates. Among them, 9 neonates were PA/IVS and 19 neonates were CPS/IVS. The mean follow-up time was 18.8 ± 5.22 months and there were no death. The ages at admission and at the first treatment were significantly younger in the prenatal diagnosis group than those in the postnatal diagnosis group (P < 0.05). At admission, the hemodynamic parameters were more stable in the prenatal diagnosis group than those in the postnatal diagnosis group. The incidence of complications was higher in the prenatal diagnosis group than that in the postnatal diagnosis group. During the follow-up period, the rate of re-intervention, the situation of the double ventricular circulation, and the development of the right ventricle and pulmonary valve at one year after surgery were no difference between two groups (P > 0.05). Conclusion Prenatal diagnosis is helpful for the early intervention in neonates with PA/IVS and CPS/IVS, and can reduce the complications after surgery.