The modified Blalock-Taussig (BT) shunt is a palliative surgery which can help the tetralogy of Fallot (TOF) patient increase the blood oxygen saturation by interposing a systemic-to-pulmonary artery shunt. Two typical anastomotic shapes are frequently used in clinical practice: the end-to-side (ETS) and the side-to-side (STS) anastomosis. This paper examines the hemodynamic influence of the anastomotic shape in the modified BT shunt. Three models with different anastomotic shapes were reconstructed. The ETS anastomoses were applied in the first model. For the innominate artery (IA) and the pulmonary artery (PA) in the second model, the ETS and the STS anastomosis were applied, respectively. Finally, the STS anastomoses were applied in the third model. The 0D/3D coupling method was used to perform a numerical simulation by coupling the three-dimensional (3D) artery model with a zero-dimensional (0D) lumped parameter model for the cardiovascular system. The simulation results showed that the perfusion into the left and right PA in Model 1 was unbalanced. Swirling flow appeared in the shunt in Model 3, but the shunt flow rate in Model 3 was lower. The ETS anastomosis at the PA may cause unbalanced blood perfusion into the left and right PA. Conversely, the STS anastomosis can make the blood perfusion more balanced. Otherwise, the STS anastomosis at the IA could generate a swirling flow in the shunt which may provide a better hemodynamic environment while decreasing the pulmonary perfusion.