Restructuring is ubiquitous in thermocatalysis and of pivotal importance to identify the real active site, yet it is less explored in electrocatalysis. Herein, by using operando X-ray absorption spectroscopy in conjunction with advanced electron microscopy, we reveal the restructuring of the as-synthesized Cu-N4 single-atom site to the nanoparticles of ∼5 nm during the electrochemical reduction of nitrate to ammonia, a green ammonia production route upon combined with the plasma-assisted oxidation of nitrogen. The reduction of Cu2+ to Cu+ and Cu0 and the subsequent aggregation of Cu0 single atoms is found to occur concurrently with the enhancement of the NH3 production rate, both of them are driven by the applied potential switching from 0.00 to -1.00 V versus RHE. The maximum production rate of ammonia reaches 4.5 mg cm-2 h-1 (12.5 molNH3 gCu-1 h-1) with a Faradaic efficiency of 84.7% at -1.00 V versus RHE, outperforming most of the other Cu catalysts reported previously. After electrolysis, the aggregated Cu nanoparticles are reversibly disintegrated into single atoms and then restored to the Cu-N4 structure upon being exposed to an ambient atmosphere, which masks the potential-induced restructuring during the reaction. The synchronous changes of the Cu0 percentage and the ammonia Faradaic efficiency with the applied potential suggests that the Cu nanoparticles are the genuine active sites for nitrate reduction to ammonia, which is corroborated with both the post-deposited Cu NP catalyst and density functional theory calculations.