Herein, we implemented complementary operando timeresolved X-ray absorption spectroscopy (XAS) and Raman spectroscopy to establish a comprehensive understanding of the true catalytically active species and sites in CoSe2 catalysts for overall water electrolysis. Three main materials, namely o-CoSe2, c-CoSe2, and c-CoSe2 with partial sulphur substitution (denoted as c-S-CoSe2), were synthesized and selected as model catalysts to in situ unravel the critical influence of phase engineering on the structural kinetics of CoSe2 for water electrolysis in different media. For the first time, our operando results unravel distinct electrochemically driven restructuring behaviors in o-CoSe2 for the HER under varying pH conditions. Specifically, under acidic conditions, o-CoSe2 undergoes a preactivation process with the removal of surface oxidized oxyanions, after which the reconstructed o-CoSe2 retains its structural integrity throughout the entire HER. In sharp contrast, for the alkaline HER, the pre-activation process promotes surface oxidation of anionic species and facilitates an exchange reaction between these oxidized species and the electrolytes. Subsequently, cathodic polarizations trigger an electrochemically driven restructuring, generating metallic Co species that act as the true catalytically active species. Notably, such pH-dependent restructuring phenomena are absent in c-CoSe2 and c-S-CoSe2 during the HER, highlighting the significance of phase engineering in regulating the reaction kinetics. As for the OER, our results corroborate that in situgenerated defective CoO2 species contribute to the intrinsic OER activities of all CoSe2 catalysts. Additionally, surface oxidized anionic components undergo complete dissolution into the electrolyte and do not contribute to the OER. This conclusion is further supported by our OER characterizations performed on reference o-CoSe2 catalysts with partial phosphorus incorporation (denoted as o-P-CoSe2) under identical reaction conditions. Furthermore, combined operando monitoring and DFT calculations allow us to establish a detailed intrinsic structure-activity relationship in CoSe2 catalysts for water electrolysis under operational conditions.