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Development of novel catalysts for nitrogen reduction at ambient pressures and temperatures with ultrahigh ammonia (NH3) yield and selectivity is challenging. In this work, an atomic catalyst with separated Pd atoms on graphdiyne (Pd-GDY) was synthesized, which shows fascinating electrocatalytic properties for nitrogen reduction. The catalyst has the highest average NH3 yield of 4.45 ± 0.30 mgNH3 mgPd−1 h−1, almost tens of orders larger than for previously reported catalysts, and 100% reaction selectivity in neutral media. Pd-GDY exhibits almost no decreases in NH3 yield and Faradaic efficiency. Density functional theory calculations show that the reaction pathway prefers to perform at the (Pd, C1, C2) active area because of the strongly coupled (Pd, C1, C2), which elevates the selectivity via enhanced electron transfer. By adjusting the p–d coupling accurately, reduction of self-activated nitrogen is promoted by anchoring atom selection, and side effects are minimized. [ABSTRACT FROM AUTHOR]