Objective To investigate the effects from various angles between inferior vein cava (IVC) and right hepatic vein (RHV) on pathogenesis of IVC membranous obstruction for patients with Budd-Chiari syndrome (BCS). Methods The normal 3D solid model of IVC and hepatic veins was reconstructed using MRI angiograms, and the angle between IVC and RHV was 56°. The two models with IVC-RHV angle of 30° and 120° were established, respectively, based on the reconstructed model. The distributions of wall shear stress, static pressure and blood velocity of the 3 models were calculated by numerical simulation. Results The wall shear stresses, static pressure and blood velocity of the 3 models displayed significantly differences. Compared with the normal 56° model, the 30° model showed a higher wall pressure and lower blood velocity, while the 120° model presented a lower wall pressure and blood velocity with turbulence of blood flowing, and such hemodynamic changes would increase the risk of thrombosis. The 56° model had the fastest blood velocity. Conclusions Numerical simulation of the flow in IVC and RHV can promote to discover the pathogenesis of BCS, and help to predict risk of IVC membranous obstruction, and provide theoretical references for BCS treatment.