Background: Both systemic-to-pulmonary shunt and right ventricle-pulmonary artery (RV-PA) connection are extensively applied to initially rehabilitate the pulmonary artery in pulmonary atresia with the ventricle septal defect (PA/VSD). However, which of these options is the most ideal for promoting pulmonary artery development and improving outcomes remains controversial. Methods: A total of 109 PA/VSD patients undergoing initial rehabilitative surgery at Guangdong Provincial People’s Hospital from 2010 to 2020 were enrolled in this study. A series of clinical data were collected to compare the perioperative and postoperative outcomes between systemic-to-pulmonary and RV-PA connection. Results: The mean duration of follow-up was 61.1 months in the systemic-to-pulmonary shunt group and 70.3 months in the RV-PA connection group (p > 0.05). The RV-PA connection technique resulted in a significantly higher PaO{}_2, lower red blood cells (RBC), lower hemoglobin, and lower hematocrit (Hct) (p 0.05). The cumulative incidence curve estimated a cumulative complete repair rate of 56 \pm 7% after 5 years in the RV-PA connection group, significantly higher than 36 \pm 7% after 5 years in the systemic-to-pulmonary shunt group (p 0.05). The Kaplan-Meier curve revealed a similar estimated survival rate between the two groups (p = 0.73). The RV-PA connection was identified as an independent predictor for complete repair in the multivariable analysis (HR = 2.348, 95% CI = 1.131–4.873). Conclusions: The RV-PA connection is a more ideal initial rehabilitative technique than systemic-to-pulmonary shunt in treating PA/VSD as a consequence of comparable probability of survival but improved definitive complete repair rate.