Electrocatalytic nitrate reduction to ammonia (NO3RR) not only effectively removes the nitrate contamination from the wastewater but also provides high-valued ammonia products for industrial applications. The design of NO3RR catalysts with moderate hydrogen-absorbing strength is urgently needed to facilitate the complete hydrogenation of intermediate products while minimizing undesired hydrogen evolution reaction (HER). Herein, we report a surface modification strategy to optimize the performance of cobalt nanoparticles through surface Se doping (Se@Co NPs) while maintaining the metallic state of Co NPs to ensure conductivity for electron transfers. The Se@Co NPs supported on carbon nanofibers (Se@Co/CNFs) exhibit a high NH3 Faraday efficiency (FE) of 94.8% and a production rate of 3.6 mmol h−1 mgcat−1 at −0.9 V vs. RHE under ambient conditions. Theoretical calculations show that Se doping on the Co surface reduces the binding strength of Co active sites with *NO, thereby reducing the energy barriers of the rate-determining step (RDS) (*NO → *NOH) in electrocatalytic NO3RR and inhibiting the competitive HER.