Currently, the cardiovascular diseases threaten almost two in one thousand new borns all around the world. The treatment of these diseases mainly depends on the surgeons' experiences. Surgeons have to choose one of the assumed options for a patient without comparing which is more feasible. In this paper, a cardiovascular surgical planning system was proposed to help the surgeons predict the optimal surgical options using Computational Fluid Dynamics (CFD) and numerical analysis. Three significant stages were included. First, patient-specific three-dimensional anatomical model was reconstructed from CT or MRI data. Second, the reconstructed model was modified into diverse surgical options as the surgeons envisioned. Third, the modified models were imported into ANSYS or CFX for CFD simulations. Hemodynamic characters, for instance, static pressure, flow rate, wall sheer stress, total pressure, flow structure and so on can be obtained. Surgeons are able to predict the post-operation outcomes according to the results of the numerical analysis. This paper studied the Fontan procedure using in the treatment of single ventricle congenital heart defect.