Phosphide-based electrocatalysts exhibit high activities in alkaline solution toward overall water electrolysis. However, their real phases during catalysis have not been comprehensively identified, leading to improper advancement in material recognition and theoretical simulation. In this work, in situ spatially coherent transmitted X-ray diffraction and X-ray absorption spectroscopy were developed to probe Fe-doped cobalt phosphides, presenting superior catalytic activity and reaction kinetics for overall water electrolysis compared to pristine cobalt phosphides. The results showed that Fe dopants latched the crystallographic sites and stabilized the phosphide phase, which are the active species for hydrogen evolution reaction, while pristine cobalt phosphide transformed into hydroxides that impede the formation of active substances. Besides, Fe-doped cobalt phosphides swiftly converted into active-site confined oxyhydroxide for oxygen evolution reaction, achieving superb overall catalytic performance. The genuine materials unveiled during the electrocatalysis suggest that the appropriate catalytic mechanism correlates with the phase transition and crystalline transformation rate.