Ammonia (NH3) synthesis is one of the most important catalytic reactions in energy and chemical fertilizer production, which is of great significance to the sustainable development of society and the economy. The electrochemical nitrogen reduction reaction (eNRR), especially when driven by renewable energy, is generally regarded as an energy-efficient and sustainable process to synthesize NH3in ambient conditions. However, the performance of the electrocatalyst is far below expectations, with the lack of a high-efficiency catalyst being the main obstacle. Herein, by means of comprehensive spin-polarized density functional theory (DFT) computations, the catalytic performance of MoTM/C2N (TM = 3d transition metal) for use in eNRR was systematically evaluated. Among the results, MoFe/C2N can be considered the most promising catalyst due to its having the lowest limiting potential (−0.26 V) and high selectivity in the context of eNRR. Compared with its homonuclear counterparts, MoMo/C2N and FeFe/C2N, MoFe/C2N can balance the first protonation step and the sixth protonation step synergistically, showing outstanding activity regarding eNRR. Our work not only opens a new door to advancing sustainable NH3production by tailoring the active sites of heteronuclear diatom catalysts but also promotes the design and production of novel low-cost and efficient nanocatalysts.