The catalytic hydrogenation of CO2 molecule over a single Co atom incorporated nitrogen-doped graphene is investigated using dispersion-corrected density functional theory calculations. It is found that a Co adatom can be effectively stabilized over a mono- or di-vacancy defective nitrogen-doped graphene due to strong hybridization between the Co-3d and N-2p states near the Fermi level. The high energy barrier for the diffusion of Co atom suggests that the resulting structures are stable enough to be used in the hydrogenation of CO2. Our results indicate the Co atom incorporated over a mono-vacancy defective nitrogen-doped graphene (CoN3-Gr) has a large tendency to activate H2 and CO2 molecules due to localization of a relative large positive charge on the Co atom. The hydrogenation of CO2 over CoN3-Gr starts with the coadsorption of H2 and CO2, followed by the formation of a formate (HCOO) intermediate. This needs an activation energy of 0.31 eV, which indicates it can easily proceed at ambient temperature. In the next step, the HCOO moiety is converted to HCOOH by overcoming an energy barrier of 0.51 eV. Our results indicate that the formation of side products, i.e. CO and H2O, is almost impossible or proceeds with great difficulty due to the corresponding large activation energy. The results of this study suggest that CoN3-Gr can be regarded as a highly active and promising catalyst for hydrogenation of CO2 at room temperature.