Non-precious Fe/N co-modified carbon electrocatalysts have attracted great attention due to their high activity and stability in oxygen reduction reaction (ORR). Compared to iron-free N-doped carbon electrocatalysts, Fe/N-modified electrocatalysts show four-electron selectivity with better activity in acid electrolytes. This is believed relevant to the unique Fe–N complexes, however, the Fe–N structure remains unknown. We used o,m,p-phenylenediamine as nitrogen precursors to tailor the Fe–N structures in heterogeneous electrocatalysts which contain FeS and Fe3C phases. The electrocatalysts have been operated for 5000 cycles with a small 39 mV shift in half-wave potential. By combining advanced electron microscopy and Mössbauer spectroscopy, we have identified the electrocatalytically active Fe–N6 complexes (FeN6, [FeIII(porphyrin)(pyridine)2]). We expect the understanding of the FeN6 structure will pave the way towards new advanced Fe–N based electrocatalysts.