The systemic-to-pulmonary artery shunt is an effective procedure widely used in the therapy of congenital heart defect (CHD). To better understand the local flow features may provide hemodynamic information for patient-specific surgical design. Here, we report on three-dimensional (3D) hemodynamic analysis of two schemes of this procedure; the modified Blalock-Taussig shunt (MBTS) and Melbourne shunt. A patient-specific 3D model after the MBTS was reconstructed. We applied the technique of computer-aided design (CAD) to virtually create a model of Melbourne shunt based on vascular anatomical position. Pressure drop, wall shear stress (WSS), streamlines and blood flow distribution ratio were calculated by computational fluid dynamics (CFD). We found more blood distribution and high pressure were observed at pulmonary artery in Melbourne shunt. This indicates to control the balance of blood flow distributed to systemic and pulmonary circulation small size shunt will be more favorable in the procedure of Melbourne shunt. The choice of surgery schemes for patient-specific surgery can be done by the analysis local hemodynamics.