Computational fluid dynamics (CFD) is one of available methods to quantitatively evaluate the treatments of cardiovascular disease. However, currently, applications of this technology to cardiac surgery are few due to the complexity of performing physiological simulation. Here, we used CFD to study the outcome of the Norwood surgical procedure for palliating hypoplastic left heart syndrome in a 33-month-old child. The Reynolds number for post-surgical flow calculated at the peak of systole was about 4000, consistent with turbulent flow. During diastole, by contrast, the flow reduced to low speed, suggesting the strong transition flow from systole to diastole. Therefore, to improve the simulation of transitional flow, we determined that time step intervals of 10-5 second were best in using the k-ε turbulence model. We also develop a new boundary condition to simulate blood pressure wave reflection from peripheral vessels in order to physiologically capture pressure recovery and correctly obtained flow through each arch-branch and flow pattern in the coronary. Then we computed time-varying energy losses, local pressure, and wall shear stress at the anastomosis to evaluate the surgical outcome. The results suggest the time step and boundary conditions that take account of pressure wave reflection improve simulation of cardiovascular flow.