Electrocatalytic nitrate reduction reaction (NO3−RR) is a green and competitive method for removing nitrate from water, requiring highly active and long-term stable electrocatalysts. In this work, we report a Cu0 nanorod catalyst with disordered structure (re-Cu NRs), prepared by electrochemical in situ reconfiguration of copper-based nitrides (Cu3N NRs). The amorphous structure allows the exposure of abundant active sites to enhance the electrocatalytic activity because of the disordered atomic arrangement. At a potential of −1.2V vs. Ag/AgCl, the re-Cu NRs catalyst achieved nearly 100% nitrate conversion within 120 min at a low nitrate concentration (50 mg/L), without the accumulation of nitrite. In-situ DEMS detection reveals that the NO3−RR on re-Cu NRs followed the pathway of *NO3− → *NO2− → *NO → *N → *NH → *NH2 → *NH3. Furthermore, combining this proposed pathway with electrochlorination could efficiently transform ammonia into harmless N2 (∼99.41%). Theoretical calculations confirm that the amorphous structure on the surface of re-Cu NRs catalysts can facilitate strongly adsorbed nitrate, weaken the rate-determining step of *NH3 → NH3, and suppress Hydrogen evolution reaction (HER). This study provides a new approach for designing efficient and stable amorphous catalysts for electrocatalytic nitrate reduction.