Nitrogen vacancy (NV) color centers in diamond have useful applications in quantum sensing and fluorescent marking. They can be generated experimentally by ion implantation, femtosecond lasers, and chemical vapor deposition. However, there is a lack of studies of the yield of NV color centers at the atomic scale. In the molecular dynamics simulations described in this paper, NV color centers are prepared by ion implantation in diamond with pre-doped nitrogen and subsequent annealing. The differences between the yields of NV color centers produced by implantation of carbon (C) and nitrogen (N) ions, respectively, are investigated. It is found that C-ion implantation gives a greater yield of NV color centers and superior location accuracy. The effects of different pre-doping concentrations (400–1500 ppm) and implantation energies (1.0–3.0 keV) on the NV color center yield are analyzed, and it is shown that a pre-doping concentration of 1000 ppm with 2 keV C-ion implantation can produce a 13% yield of NV color centers after 1600 K annealing for 7.4 ns. Finally, a brief comparison of the NV color center identification methods is presented, and it is found that the error rate of an analysis utilizing the identify diamond structure + coordination analysis method is reduced by about 7% compared with conventional identification methods.