Currently, the modified Blalock-Taussig (mB-T) shunt is the most preferred surgery served as the first step of the staged procedures in the treatment of cyanotic congenital heart defect. A Gore-Tex conduit is used to surgically connect the systemic and pulmonary circulations. In the present study, we report on three-dimensional (3D) hemodynamic analysis of the effects of conduit anastomosis angles on hemodynamics of the mB-T shunt. We constructed a patient-specific 3D model after the mB-T shunt based on medical images and employed computer-aided design to reconstruct two new models with different anastomosis angles. The local pressure, blood flow distribution and wall shear stress were calculated. The results suggest the scheme of vertical anastomosis angle of the conduit on the pulmonary artery can increase the blood flow distribution from systemic circulation to two lungs and blood flows more smoothly in the conduit. The results are well congruent with our clinical experience. This indicates the numerical methods may be applied to investigate hemodynamics of the mB-T shunt for different surgical schemes.