Electrochemical reduction of nitrogen is considered a promising route for achieving green and sustainable ammonia synthesis under ambient conditions. A transition metal atom loaded on N-doped graphene is commonly used in the nitrogen reduction reaction (NRR), but the effect of the graphene's coordination environment on electron transfer has rarely been studied. Herein, the NRR performance of Fe1/2/3 clusters, anchored on single-vacancy and N-doped graphene, is investigated systematically via density functional theory (DFT). The calculation results show that the Fe2 cluster supported by two N atom-modified single-vacancy graphene displays the highest catalytic performance of NRR with the lowest energy barrier of 0.62 eV among the 12 candidates, and exhibits efficient selectivity. It has superior performance because of the highly asymmetrical distribution of electrons on graphene, the large positive charge of the Fe2, and the strong adsorption of *NNH. This study provides a new strategy to improve the NRR performance by regulating the Fe1/2/3 clusters coordination environment.