Transition-metal-based compounds have been intensively explored as efficient electrocatalysts for hydrogen evolution reaction (HER). Feasible reconstruction to the real active sites, which is yet to be identified, endows the promotion of HER activity. Here, it is reported that the incoming S coordinates and anion vacancies prompt the structural reconstruction of S-doped Co3O4 on carbon cloth (S-Co3O4/CC) during HER. A list of in situ studies reveals that the real active sites for HER are the “metallic surface-adparticles” system embracing metallic Co scaffold and the dilute coverage of S coordinated Coδ+. Reaction mechanism exploration illustrates that interfacial perimeters between the coverage of Co3S4 moieties and metallic Co considerably facilitate the adsorption of H*, improve the kinetics of water dissociation, and consequently promote HER activity. The exemplified sulfide-mediated topotactic transformation strategy is extended to the preparation of S, Fe codoped Ni(OH)2 (S-NiFe/CC) as a bifunctional electrocatalyst. The assembled anion exchange membrane water electrolyzer achieves a current density of 1.0 A cm−2 at 1.72 V, showing excellent capability in catalyzing overall water splitting at ampere level. This study, showing a feasible strategy that enables the facile reconstruction to identify active sites, would inspire the development of efficient electrocatalysts for HER and other electrochemical hydrogenation reaction.