While FeN4 species are widely suggested as the active sites of noble-metal-free Fe–N–C oxygen reduction reaction (ORR) electrocatalysts, the ORR mechanism, particularly the rate-determining steps (RDSs) at the Fe centers, and the likely contribution of co-existed C–N active site remain disputed. Moreover, the dynamic structures of the FeN4 active sites during ORR electrocatalysis also remain elusive. By in situ (isotope-labeled) Raman spectroscopy of molecular Fe phthalocyanine (FePc) model catalysts and pyrolyzed Fe–N–C catalysts, we achieve direct, simultaneous spectral identification of the ORR intermediates/RDSs at different active sites under different pH conditions, from which their intrinsic activities and ORR mechanisms can be quantitatively decoupled. Besides the single-atomic Fe–Nx site, two kinds of C–N sites were pinpointed and clarified as separate active sites in pyrolyzed Fe–N–C catalysts, showing different ORR intermediates (*O2– and *OOH) and RDSs. Furthermore, from the FePc model catalyst, we reveal a pH-dependent structural switching of the FeN4 between planar and non-planar structures during ORR electrocatalysis, which provides important insights into their pH-dependent ORR activity (RDS) and stability.