The further rupture of atherosclerotic ulceration plaque is one of the main triggers of the carotid ischemic stroke. However, the abnormal hemodynamics is not well addressed yet. A lesion-based computational fluid dynamic (CFD) analysis is proposed to investigate the complex hemodynamic change of the ulceration plaque that prevails in patients. The 3D models including eight groups of ulcerations (six groups with single ulceration and two groups with two consecutive ulcerations), were reconstructed based on the computer tomography (CT) images, and the tetrahedral grid was taken to mesh the models with the appropriate numbers. After setting the boundary conditions, numerical simulation was carried out to analyze the pulsatile blood flow in the models. The complex flow in the vicinity of the ulcerations directly leads to a significant effect on the distribution of the wall shear stress (WSS). WSS is respectively from 3.29 to 35.41 Pa at the upstream, from 11.90 to 41.85 Pa at the downstream ulceration, and 18.60 and 30.60 Pa in the area between the two consecutive ulcerations. The rupture from these regions could cause the further rupture of ulceration plaques, particularly at the downstream ulceration and the area between the two consecutive ulcerations. The twisting and the curling of the flow at the ulcerations can lead to thrombosis which may break free later and go through the downstream stenosis by the effect of the flow. The different degrees of WSS in downstream and upstream ulcerations will damage the ulceration on the plaque because of pulling and stretching forces at the ulcerations. Furthermore, high wall shear stress gradient (WSSG) also increases the risk of the further rupture. Our study gives a better understanding in the further rupture mechanism of ulceration plaques and provides the information of the location of thrombosis after aggravated rupturing, which can be referred by surgeons to improve the surgical planning.