Charged natural chalcopyrite (CuFeS2, Ncpy) was developed for a three-dimensional electrochemical nitrate reduction (3D ENO3−RR) system with carbon fiber cloth cathode and Ti/IrO2 anode and Zn-NO3− battery. The 3D ENO3−RR system with Ncpy particle electrodes (PEs) possessed superior nitrate removal of 95.6 % and N2 selectivity of 76 % with excellent reusability under a broad pH range of 2–13 involving heterogeneous and homogeneous radical mechanisms. The Zn-NO3− battery with Ncpy cathode delivered an open-circuit voltage of 1.03 V and a cycling stability over 210 h. It was found that Ncpy PEs functioned through self-oxidation, surface dynamic reconstruction (Cu1.02Fe1.0S1.72O1.66 to Cu0.61Fe1.0S0.27O2.98), intrinsic micro-electric field (CuI, S2− anodic and FeIII cathodic poles), and reactive species (•OH, SO4•−, 1O2, •O2− and •H) generation. Computational analyses reveal that CuFeS2(112) surface with the lowest surface energy preferentially exposes Fe and Cu atoms. Cu site is beneficial for reducing NO3− to NO2−, Fe and Fe−Cu dual sites are conducive to N2 selectivity, lowering the overall reaction barriers. It paves the way for selective NO3− reduction in wastewater treatment and can be further extended to energy storage devices by utilizing low-cost Ncpy.