Hypoplastic left heart syndrome (HLHS) is a congenital heart disease which should be treated at neonate. Even now, its operation is one of the greatest challenges. However, currently there are no quantitative standards to evaluate and predict the outcome of the therapy. In this study, computational fluid dynamics (CFD) was used to estimate the performance of first stage HLHS surgery, the Norwood operation. An image data transfer system was developed to convert clinical images into three-dimensional geometry. To confirm software applicability, a validation process was carried out to eliminate any influence of numerical procedures. The velocities derived from echocardiography measurements were used as boundary conditions, and pressure waves measured by a cardiac catheter simultaneous with an electrocardiogram (ECG) were employed to validate the results of CFD simulation. Calculated results were congruent with the in vivo measurement results. The blood flow circulations were successfully simulated and the distribution of blood flow in each vessel was estimated. Time-varying energy losses (EL), local pressure and wall shear stress (WSS) were analyzed to estimate clinical treatment. The results indicated that pulsatile simulation is essential in quantitative evaluation. Computational hemodynamics may be applied in the surgical optimization for the treatment of HLHS.