Objective To investigate the mechanical effect of stents with different links on the treatment of vertebral artery stenosis, and provide scientific guidelines for the design of stent structure and clinical procedure of stenting intervention. Methods Models of three kinds of stents with different types of links (namely, L-stent, V-stent and S-stent according to the shape of links) and vertebral artery with stenosis were established by using Pro/Engineering, then the same boundary conditions were exerted on the three models to simulate the stent deployed in the vertebral artery by finite element analysis using ABAQUS. Results Compared with L-stent and V-stent, S-stent had a better compliance, generating smaller stress in the arterial wall, causing relatively weak vascular straightening. Due to smaller stress and axial shortening generated in the stent strut, S-stent made less lesion on the arterial wall. Conclusions The therapeutic effect of S-stent is the best among the three kinds of stents, which could reduce in-stent-restenosis, and has good prospect in clinical application.