Atomistic‐level understanding of electrocatalytic mechanism is pivotal to developing amorphous/crystalline heterostructures for highly efficient overall water splitting (OWS). Herein, an amorphous‐crystalline Ni3S2/Cu heterojunction (a‐Ni3S2/Cu) is constructed through a facile one‐step strategy. Benefiting from the tailored local microenvironment, the catalyst shows superior performance with ultralow overpotentials of 26 mV for hydrogen evolution reaction (HER) and 219 mV for oxygen evolution reaction (OER), and needs a cell voltage of merely 1.49 V for OWS at 10 mA cm−2 in alkaline electrolyte, alongside distinguished long‐term stability. Advanced characterizations combined with first‐principles calculations reveal that the positive charge accumulation on S sites successfully activates water molecules, while the upward shift of the d‐band center over Cu sites balances the adsorption/desorption of H* intermediates, thus reducing energy barrier of HER determining step. Furthermore, strong interfacial coupling enables a structural reconstruction, forming NiOOH as OER active centers. In situ Raman spectrum coupled with 18O isotope labelling experiments confirm that the reconstructed surface on a‐Ni3S2/Cu follows the adsorbate evolution mechanism. The formed Ni3+ sites optimize the adsorption of *OH intermediates, thereby accelerating the OER kinetics. This work provides atomistic insights into the structure‐performance relationship in amorphous/crystalline heterostructures, paving the way for designing next‐generation catalysts.