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Background This study aimed to evaluate neonatal surgical outcomes of patients diagnosed with complex congenital heart disease (CHD) during pregnancy and treated by the newly initiated “perinatal integrated diagnosis and treatment program (PIDTP)”.Methods We reviewed clinical data of 207 neonates (surgical age ≤ 28 days) who underwent cardiac surgeries in a single center from January 2017 to December 2018,including 31 patients with referrals from the “PIDTP” (integration group) and 176 patients with routine referral treatment (non-integrated group).Results In the integration group,median admission age was 0 days and median age at surgery was 4 days.In the non-integrated group,median admission age was 8 days (P =0.001) and median age at surgery was 13 days (P =0.001).The emergency surgery rate in patients with duct-dependent defects was 36％ in the integration group and 59％ (P =0.042) in the non-integrated group,respectively.The in-hospital mortality was 16％ in the integration group and 14％ (P=0.78) in the non-integrated group.The 2-year cumulative survival rate after surgery was 83.9％ ± 6.6％ in the integration group and 80.3％ ± 3.1％ (P =0.744) in the non-integrated group.According to multivariable regression analysis,independent risk factors for early mortality of overall neonatal cardiac surgery were low body weight,high serum lactate level,postoperative extracorporeal membrane oxygenation (ECMO) support and prolonged cardiopulmonary bypass (CPB) time.Conclusions PIDTP shortens the postnatal transit interval,reduces the emergency operation rate of neonatal critical CHD,and provides better preoperative status for surgery.Patients treated by the PIDTP tend to have more complicated anatomical deformity and a greater requirement for the operation and postoperative management,but early outcome and follow-up prognosis are satisfactory.