Revealing the dynamic reconfiguration of catalysts and the evolution of active species during catalysis, elucidating and regulating the reconfiguration mechanism are paramount to the development of high-performance electrochemical nitrate reduction (NO3RR) to ammonia. In-situ characterizations can precisely track reaction process and unveil the origin of activity enhancement. Here, in-situ reconstruction of pre-catalyst Co3O4 fabricates a stable heterojunction Co(OH)2/Co3O4 to boost NO3RR to ammonia. In-situ generated heterojunction accelerates the transformation of *NO3 to *NO2, while Co(OH)2 promotes the dissociation of water to active *H species for the hydrogenation of *N species, and thereby improving the deoxygenation and hydrogenation ability of NO3RR to NH3 and achieving a high Faradaic efficiency (FE) about 96.2% and a high NH3 production rate of 218.5 μmol h−1 mgcat−1 at −0.3 V. Density functional theory (DFT) calculations verified that in-situ formed active species Co(OH)2 on Co3O4 markedly decreased the energy barrier of *NO3 → *NO2 and accelerated the hydrogenation step of *NH → *NH2 → *NH3. Co(OH)2/Co3O4 heterostructure-based Zn-NO3− cell achieves excellent energy supply (1.22 V), a high ammonia yield rate (48.9 µmol h−1 cm−2), and a high FE (91%). The establishment of the structure–activity relationship during NO3RR provides guidance for designing advanced electrode materials, and the in-situ evolution of species on the electrode surface unveils the intrinsic nature of improved catalytic performance.