AbstractThe manipulation of surface catalytic sites has rarely been explored for metal borides, and the subsurface effects on the electrocatalytic activity of the nitrogen reduction reaction (NRR) remain unknown. Herein, this work develops a core–shell nanoparticle catalyst with a Pd core that ensures high electron transfer rates and an Pd16B3 atomical shell that possess tunable active sites for regulating the NRR. The atomic structural evolution from Pd to Pd16B3 is investigated by precisely controlling the B atom diffusion, molecular rearrangement, and d–sp orbital hybridization. Pd/Pd16B3 core–shell nanocrystals exhibit an exceptional NRR performance with a high NH3 Faradaic efficiency of 30.8%, which is superior to those of pristine Pd (1.2%) and B‐doped Pd (4.8%) under identical conditions, and a yield rate of 0.81 µmol h−1 cm−2. This work discovers that the Pd16B3 shell could promote the NRR selectivity by separating the separating the hydrogen evolution reaction proceeded on hole sites and NRR proceeded on bridge sites, and the Pd core could provide the excellent conductivity to Pd16B3 shell through regulated electron interactions. Consequently, the controlled chemical ordering of palladium boride on palladium surfaces provides insight into the synthesis of advanced NRR electrocatalysts.