The discovery of the "two birds, one stone" electrochemical nitrate reduction reaction (NO3RR) allows for the removal of harmful NO3− pollutants as well as the production of economically beneficial ammonia (NH3). However, current understanding of the catalytic mechanism of NO3RR is not enough, and this research is still challenging. To determine the mechanism needed to create efficient electrocatalysts, we thoroughly examined the catalytic activity of molybdenum-based diatomic catalysts (DACs) anchored on two-dimensional carbon-rich conjugated frameworks (2D CCFs) for NO3RR. Among the 23 candidate materials, after a four-step screening method and detailed mechanism studies, we discovered that NO3RR can efficiently generate NH3 by following the N-end pathway on the MoTi-Pc, MoMn-Pc, and MoNb-Pc, with limiting potential of −0.33 V, −0.13 V, and −0.38 V, respectively. The activity of NO3RR can be attributed to the synergistic effect of the TM1-TM2 dimer d orbital coupling to the anti-bonding orbital of NO3−. Additionally, high hybridization between the Mo-4d, TM-3d(4d), and NO3−-2p orbitals on the MoTMs-Pc DACs can speed up the flow of electrons from the Mo-TM dual-site to NO3−. The research presented here paves the way for the reasonable design of effective NO3RR catalysts and offers a theoretical basis for experimental research.