Objective To investigate the in vivo stress distribution of the atherosclerotic plaque at carotid bifurcation, so as to provide references for the mechanical mechanisms of plaque rupture at carotid bifurcation and the design for further medical treatment. Methods The three-dimensional geometric model of carotid bifurcation and plaque were established according to average geometric parameters of human carotid bifurcation. Residual stress of the carotid bifurcation and plague was reestablished with “thermal-structure” coupling method, and in vivo stresses of vessels with the plaque at carotid bifurcation under blood pressure and blood flow were calculated. Results Both the maximum principal stress and elastic shear stress concentrated on the shoulder of the plaque. Elastic shear stress increased with the increase of stenosis ratio and blood pressure. Wall shear stress in the upstream of the plaque was considerably higher than that of the downstream. The distribution of oscillatory shear index(OSI) was quite the opposite. The changing patterns of the elastic shear stress and flow shear stress were quite different with the change of stenosis ratios. Conclusions Tension grew gradually from the centrality to shoulder surface of the plaque. The centrality of the plaque might bear compression when the stenosis was very severe. The periodic variation of the structural stress might cause structural fatigue of the plaque, thus increasing the rupture risk. Distinction of the component and vulnerability of the plaque between upstream and downstream might be caused by differences in hemodynamic parameters of the plaque between upstream and downstream.