Objective In the computational fluid dynamics software FLUENT, the independently developed user defined function (UDF) dynamic mesh program is called to achieve the mobile update of grid note based on the wall shear stress (WSS). Then this method is applied to simulate the development process of atherosclerosis (AS). Methods The UDF program by secondary development could extract WSS results of every note on the wall during the computing process, and if the threshold value criterion condition was met, the node would be adjusted to a new position. The mesh regeneration method combining with the spring smoothing and the local remeshing was adopted to control the update of the grid, so as to ensure the grid quality during deformation. Results The UDF program successfully extracted the WSS and arranged the corresponding deformation for the grid. The morphology of local extension in the proximal part and restenosis in the distal end were resulted from the vortex in the rear of the initial stenosis. Those features were similar to the indication of clinical angiography. Conclusions The independently developed UDF program has reached the expected effects, depicting the topography characteristics of AS influenced by WSS. In future researches, more influential factors should be considered in dynamic mesh deformation control to provide numerical references for clinical prognosis and risk evaluation of AS.