Objective: The systemic-to-pulmonary shunt (SPS) and right ventricle to pulmonary artery (RV-PA) connection were evaluated to pursue the goal of rehabilitating dysplastic native PAs via establishment of antegrade blood flow. However, the application of these two palliative operations was still confusing. We compared the two operations to determine their different effects on patients who have pulmonary atresia, ventricular septal defects, and major aortopulmonary collateral arteries (MAPCAs). Methods: From January 2011 to January 2016, 44 patients received the SPS procedure, and 54 patients received the RV-PA connection procedure; these procedures were compared based on perioperative data and follow-up data. There was no significant difference between the two groups for follow-up time (15.5 ± 11.8 vs 11.4 ± 10 months; P =.073). Results: The SPS patients had a smaller preoperative pulmonary artery index (68.57 ± 38.25 vs 112.62 ± 61.63 mm2/m2; P <.01), more MAPCAs (2.4 ± 1.1 vs 1.8 ± 1.5; P =.045) and had a shorter intubation time (26.73 ± 27.20 vs 40.88 ± 36.93 hours; P =.045), intensive care unit stay (3.6 ± 3.9 vs 5.7 ± 5.5 days; P =.033), and hospital stay (9.9 ± 3.9 vs 14.7 ± 11.9 days; P =.014) than the RV-PA connection patients. The cumulative complete repair rate and cumulative survival rate did not differ significantly between the two groups. Conclusions: Both the SPS and the RV-PA connection could rehabilitate the PA and produce complete repair, while the SPS could achieve better early postoperative outcomes and be suitable for patients with severe dysplastic PAs and large MAPCAs. © 2019 Wiley Periodicals, Inc.