Objective To predict the influence of connecting position between left superior vena cava (LSVC) and pulmonary artery on bilateral bidirectional Glenn (BBDG) shunt by numerical simulation. Methods Firstly, a 3D anatomical geometrical model was reconstructed by the medical images of a hypoplastic left heart syndrome (HLHS) patient with LSVC. Secondly, based on haptic deformations, several computational models were virtually generated, and computational fluid dynamics (CFD) numerical simulations were conducted using finite volume method. Finally, hemodynamic parameters were analyzed and evaluated. Results Flow recirculation was observed in the pulmonary artery between the LSVC and right superior vena cava (RSVC). The diameter of RSVC was defined as D. Varying the distance between LSVC and RSVC from 2D to 3.5D resulted in the least energy dissipation at 3D and the most at 2D. The blood flow rate ratios of left pulmonary artery to right pulmonary artery (LPA/RPA) ranged from 0.65-1.11. Conclusions Too close distance between LSVC and RSVC would bring out unfavorable hemodynamic distributions and consume more energy in the treatment of BBDG shunt. This study is of significance for surgeons to evaluate the optimal Fontan options in the treatment of HLHS accompanied by LSVC.