The low arterial oxygen saturation (SaO₂) after bidirectional cavopulmonary shunt (BCPS) predicts poor prognosis. The venous oxygen saturation of inferior vena cava (SivcO₂), as well as the pulmonary blood flow/systemic blood flow ratio (Q _p/Q _s) affects the SaO₂. The purpose of this study is to determine whether SivcO₂ or Q _p/Q _s should be increased to achieve better outcomes after BCPS. Forty-eight patients undergoing BCPS were included. Data of patients’ age and body weight, SivcO₂, Q _p/Q _s, pulmonary artery (PA) pressure and resistance, PA area index, morphology of ventricle, atrioventricular valve regurgitation, and history of PA plasty were collected. Stepwise multiple logistic regression analyses were used to investigate which of the factors most affected the SaO₂ after BCPS. There was a significant correlation between SivcO₂ and SaO₂ (r = 0.771, P < 0.00001). There was no strong correlation between Q _p/Q _s and SaO₂ (r = 0.358, P < 0.05). Stepwise multiple logistic regression analyses revealed that both SivcO₂ (r = 0.49, 95 % confidence interval (CI) 0.37–0.62, P < 0.0001) and Q _p/Q _s (r = 11.1, 95 % CI 3.3–18.9, P = 0.007) most affected SaO₂ after BCPS. Since the SivcO₂ has a stronger correlation than Q _p/Q _s with SaO₂, despite the fact that both raising Q _p/Q _s and raising cardiac output can increase SaO₂, raising cardiac output should be considered prior to Q _p/Q _s to raise the SaO₂ after BCPS.