Molecular dynamics (MD) simulations with a quantum correction were used to study the 0.5 mol% V5+/TiO2 rutile under conditions of 300 K and 101 kPa. The interatomic potential function in MD simulations is composed of Coulomb, short-range repulsion, van der Waals, and Morse interactions. The topology of rutile was found to undergo a large deformation when Ti4+ is replaced by V5+, which can be related to the difference of valence and ionic radius between V5+ and Ti4+. The graphed distributions of Ti-O and O-O bond lengths, and O-Ti-O angles are all broaden. The simulations showed that when Ti4+ is replaced by V5+, the V5+ moves out of the O6 polyhedron and toward the interstice between TiO6 octahedra, which results in serious distortion of the octahedra near the interstice, but the phase with 0.5 mol% V5+ doping still remains in rutile. The structural features, such as the bond lengths, migration of the dopant, and crystal phase in the MD simulation are consistent with the experimental observations by FTIR, Raman, XRD and ESR.