Understanding radiation-induced defect formation in carbon materials is crucial for nuclear technology and for the manufacturing of nanostructures with desired properties. Using first-principles molecular dynamics, we perform a systematic study of the nonequilibrium processes of radiation damage in graphite. Our study reveals a rich variety of defect structures (vacancies, interstitials, intimate interstitial-vacancy pairs, and in-plane topological defects) with formation energies of 5–15 eV. We clarify the mechanisms underlying their creation and find unexpected preferences for particular structures. Possibilities of controlled defect-assisted engineering of nanostructures are analyzed. In particular, we conclude that the selective creation of two distinct low-energy intimate Frenkel pair defects can be achieved by using a 90–110 keV electron beam irradiation.