Density functional theory calculations have been performed to study the reaction mechanism of N2 thermal reduction (N2TR) over a single metal atom incorporated nitrogen-doped graphene. Our results reveal that the type of metal atoms and their coordination environments have a significant effect on the catalytic activity of N2TR. Regarding CoN4- and FeN4-embedded graphene sheets that the metal atom is fourfold coordinated, they are inactive for N2TR owing to the poor stability of the adsorbed H2 and N2 molecules. In contrast, if the monodisperse metal atom is surrounded by three N atoms, namely, CoN3/G and FeN3/G show activity toward N2TR, and catalytic conversion of N2 into ammonia is achieved through the associative mechanism rather than the dissociative mechanism. Further investigations show that the synthesis of NH3 over the two surfaces is mainly through the formation of an NHNH* intermediate; however, the detailed reaction mechanisms are sensitive to the type of metal atom introduced into N-doped graphene. Based on the calculated kinetic barriers, FeN3/G exhibits a better catalytic activity for N2TR. The superior performance of FeN3/G can be attributed to the fact that this surface prefers a high spin-polarized state during the whole process of N2TR, while the non-spin polarized state is predicted as the ground state for most of the elementary steps of N2-fixation over CoN3/G. The present study provides theoretical insights into developing graphene-based single atom catalysts with a high activity toward ammonia synthesis through N2TR.