Molecular catalysis of water oxidation has been intensively investigated, but its mechanism is still not yet fully understood. This study aims at capturing and identifying key short-lived intermediates directly during the water oxidation catalyzed by a cobalt-tetraamido macrocyclic ligand complex using a newly developed an in situ electrochemical mass spectrometry (EC-MS) method. Two key ligand-centered-oxidation intermediates, [(L2-)CoIIIOH] and [(L2-)CoIIIOOH], were directly observed for the first time, and further confirmed by 18O-labeling and collision-induced dissociation studies. These experimental results further confirmed the rationality of the water nucleophilic attack mechanism for the single-site water oxidation catalysis. This work also demonstrated that such an in situ EC-MS method is a promising analytical tool for redox catalytic processes, not only limited to water oxidation.