Objective To analyze and compare hemodynamic features of two different options for modified B-T shunt (MBTS) surgery, namely end-to-side(ETS) and side-to-side (STS), so as to provide references for clinical treatment of single ventricle heart defect syndrome. Methods The real geometric model was reconstructed by medical images obtained from a patient with hypoplastic left heart syndrome (HLHS); MBTS surgery was simulated through virtual operations; a lumped parameter model (LPM) was constructed based on physiological data of the patient; the post-operational boundary conditions of computational fluid dynamics (CFD) models (namely STS model and ETS model) were predicted based on the LPM; numerical simulation was conducted on two CFD models by using finite volume method. Results Flow details and wall shear stress distributions were all obtained for two models. The mean oscillatory shear index (OSI) of ETS model and STS model in part of pulmonary arteries was 3.058×10-3 and 13.624×10-3, respectively, while the energy loss was 116.5 and 94.8 mW, respectively, and blood flow rate ratios of left pulmonary artery to right pulmonary artery (RRPA/LPA) were 0.8 and 1.72, respectively. Conclusions There were nearly no differences between two CFD models in energy loss, which led to a relatively small impact on the surgery. The STS model had a more balanced pulmonary artery blood perfusion and a smaller mean OSI in part of pulmonary arteries, therefore, the STS model was superior to the ETS model. This study provides an important theoretical support and reference for treating patients with HLHS.