Numerical analysis of cardiovascular flow is one of several methods of use for the quantitative evaluation of patient-specific treatments. However, due to the complexity of vascular geometry and flow conditions, the cardiovascular flow simulation continues to be a challenging project. As the flow at the peak of systolic heart beat displayed full turbulence, the congenital heart treatments, Norwood and TCPC procedure, were investigated through the use of computational hemodynamic technology, in the present study. On the other hand, at diastolic period, the flow fell to an almost sedentary state. This indicated that the cardiovascular flow experienced a strange transition of flow from systolic peak to diastole. Thus, in order to accurately simulate this transitional flow, a very small time step was applied in the k turbulent model calculation. Energy losses (EL), local pressure and wall shear stress were analyzed to estimate the result of clinical treatments. It was found that the value of EL, including the influence of respiration, was 1.5 times higher than the value of EL, disregarding respiratory influences. These results indicated that the hemodynamic outcomes of TCPC treatment are noticeably influenced by respiration. The effect of respiration plays an important role in estimating the results of TCPC treatment and thus should be included as one of the important conditions of computational hemodynamic analysis.