We sought to investigate the effects of endovascular stents with different links for treating stenotic vertebral artery and to determine the relationship between the shape of the link and in-stent restenosis (ISR). We also attempted to provide scientific guidelines for stent design and selection for clinical procedures. Models of three types of stent with different links (L-stent, V-stent, and S-stent) and an idealized stenotic vertebral artery were established. The deployment procedure for the stent in the stenotic vertebral artery was simulated for solid mechanics analysis. Next, the deformed models were extracted to construct the blood flow domain, and numerical simulations of the hemodynamics in these models were performed using the finite element method. The numerical results demonstrated that: (1) Compared with the L-stent and V-stent, the S-stent has a better flexibility and induces less stress in the stent strut. Furthermore, less stress is generated in the arterial wall. (2) Vascular straightening is scarcely influenced by the shape of the link, but it is closely related to the flexibility of the stent. (3) The S-stent has the smallest foreshortening among the three types of stents. (4) Compared with the V-stent and S-stent, the L-stent causes a smaller area with low wall shear stress, less blood stagnation area, and better blood flow close to the artery wall. From the viewpoint of the combination of solid mechanics and hemodynamics, the S-stent has better therapeutic effects because of its lower potential for inducing ISR and its better prospects in clinical applications compared with the L-stent and V-stent.