Few reports study the effects of the anatomical structure of the iliac vein on hemodynamics and the methods to reduce and delay in-stent thrombosis. The anatomical structure of iliac vein stenosis was used to establish vascular models with different stenosis rates, taper angle, and left branch tilt angle in the work. The influence of anatomical structure on hemodynamics was revealed through theoretical research and in vitro experimental verification. A real iliac vein model was built based on computed tomography angiography (CTA) images, and hemorheological parameters including time-averaged wall shear stress (TAWSS), oscillatory shear index (OSI) and relative residence time (RRT) were analyzed by computational fluid dynamics (CFD). The results showed that iliac vein stenosis could significantly increase the wall shear stress (WSS) of the blood vessels at the stenosis site and outside the intersection area, which was easy to produce eddy currents in the distal blood vessels. With the increased taper angle, the proportion of low-wall shear stress areas and the risk of thrombosis increased. A small tilt angle could aggravate the influence of narrow blood vessels on the blood flow characteristics and vascular wall. The numerical simulation results were consistent with the theoretical research results, and the experimental study verified the correctness of the simulation. The work is helpful to further understand the hemodynamic characteristics of the iliac vein, providing a scientific reference for clinical treatment and diagnosis.