Single-atom catalysts (SACs) exhibit higher atomic utilization, while double-atom catalysts (DACs) and triple-atom catalysts (TACs) have an advantage due to the synergistic effect of multiple atomic centers. However, the current research on the mechanism of multiple-atom catalysts in electrocatalytic nitrate reduction to ammonia (NRA) remains insufficient. Herein, we investigated a series of homonuclear single-, double-, and triple-atom catalysts on carbon phosphide (PC6) monolayers (TMn@PC6, where TM = non-noble transition metals; n = 1, 2, or 3). The NRA activity of these catalysts was assessed by the density functional theory calculations, Co3@PC6 and Ru3@PC6 exhibit superior limiting potentials of −0.34 V and −0.36 V, respectively. Their capability to produce *H with optimal free energy on their surface enhances the electrochemical potential-determining step of *NO to *NOH while simultaneously inhibiting the hydrogen evolution reaction. The movement of the d-band center, induced by metal atom doping, regulates the adsorption strength of *NO, thus achieving a lower barrier for the hydrogenation step. This work provides theoretical guidance for the development of highly efficient multiple-atom catalysts for NRA.