Percutaneous coronary intervention (PCI) is widely adopted to check and cure coronary heart disease. However, acute thrombus may occur during surgery. This study aims to numerically find out the underlying mechanism of the acute thrombus during surgery in terms of hemodynamics.Patient-specific 3D models of the coronary arteries (CA) were reconstructed based on the computed tomography scan images. And the hemodynamic parameters in the five stages of PCI guided operation were obtained under pulsatile physiological flow conditions. The results show that the intervention process resulted in changes of hemodynamics in the CAs, such as the eccentric blood flow in the CA, the increased time-averaged wall shear stress (Tawss) and the decreased oscillatory shear index (OSI). Also, the decrease in relative resistance time (RRT) for a particle and the slightly increase in transverse WSS (Transwss) were also observed, which indicates that the vascular endothelial cells are exposed to high WSS. The predispose to the thrombus formation due to the exposure to high Tawss and the eccentricity of blood flow may overweight the inhibition effect of low RRT and OSI.