Portal vein thrombosis (PVT) is an important complication that is associated with cirrhotic portal hypertension. The etiology is as yet unclear but could be closely related to the hemodynamics of the portal vein system. This paper investigated the hemodynamics in the portal vein model, both with and without thrombosis, as well as the effect of obstructions on the hemodynamics of the portal vein system using the computational fluid dynamics (CFD) method. PVT can probably develop in the inlets of the portal vein as well as the left/right branches of the portal vein because the distribution of wall shear stress satisfies the conditions for PVT formation based upon the simulation of the hemodynamics in the normal portal vein model. According to the above results, geometric models for a portal vein with a thrombus were constructed and the influence of different degrees (26%, 39%, 53% and 64%) of obstructions was studied. In the model with the maximum obstruction (64% blocked), the maximum velocity of portal vein (PV) increased up to twice than in the model without thrombosis, and the maximum wall shear stress of PV in the model with thrombosis (64% blocked) increased up to 9.4 Pa, whereas it was only 1.9 Pa in the model without thrombosis (nearly one fifth of the maximum wall shear stress). Excessive wall shear stress may cause mechanical damage to the blood vessels and induce physiological changes.