Objective To explore the feasibility of applying fractional flow reserve (FFR) into the assessment of carotid stenosis, and analyze the effects from elastic modulus of vessel wall on hemodynamic parameters of carotid artery stenosis model and FFR calculation results. Methods The standard models of carotid bifurcation and stenosis models with different stenosis rates were established by computer-aided design software. Assuming that the vessel wall was linear elastic material and the blood was incompressible Newtonian fluid, the fluid-structure coupling simulation of blood flow in carotid artery stenosis model under the pulsating flow was carried out by finite element analysis, and the relevant hemodynamic parameters were obtained, and the corresponding FFR was calculated. Results When the elastic modulus was fixed, the FFR for narrow part of the model decreased gradually with the increase of the stenosis rate, and the relative difference between the FFR of elastic wall and rigid wall increased with the increase of the stenosis rate; when the stenosis rate was fixed at 70%, the FFR decreased gradually with the increase of elastic modulus. Conclusions The effect of vascular wall elasticity should be considered in the process of functional assessment on carotid stenosis with FFR; the larger stenosis rate will lead to the greater influence from elastic modulus of vessel wall on FFR.