© 2020 The Authors. Published by Wiley-VCH GmbH Electrochemical nitrogen reduction reaction (NRR) over nonprecious-metal and single-atom catalysts has received increasing attention as a sustainable strategy to synthesize ammonia. However, the atomic-scale regulation of such active sites for NRR catalysis remains challenging because of the large distance between them, which significantly weakens their cooperation. Herein, the utilization of regular surface cavities with unique microenvironment on graphitic carbon nitride as “subnano reactors” to precisely confine multiple Fe and Cu atoms for NRR electrocatalysis is reported. The synergy of Fe and Cu atoms in such confined subnano space provides significantly enhanced NRR performance, with nearly doubles ammonia yield and 54%-increased Faradic efficiency up to 34%, comparing with the single-metal counterparts. First principle simulation reveals this synergistic effect originates from the unique Fe–Cu coordination, which effectively modifies the N2 absorption, improves electron transfer, and offers extra redox couples for NRR. This work thus provides new strategies of manipulating catalysts active centers at the sub-nanometer scale.