Exploring an efficient route to prepare novel graphene-based nanostructure of organic small molecule as metal single-atom catalyst still faces a great challenge due to the difficult synergy of complicated nanostructure for multiple catalytic steps. Herein, the iron phthalocyanine (FePc)-based nanostructures are synthesized via the graphene-assisted colloid chemical reaction for the first time. Compared to the commercial Pt/C for oxygen reduction reaction (ORR), the optimal FePc/graphene nanostructure exhibits not only more positive onset potential (Eonset, 1.000 vs 0.973 V) and half-wave potential (△E1/2 = 100 mV), but also better stability and durability in alkaline solution. The corresponding zinc-air battery also shows better the maximum power density. The systematical characterizations prove the axial coordination between FePc and graphene via Fe-O-C bond and the formation of Fe(II)Pc/Fe(III)Pc/graphene nanostructures. The comprehensive analysis and simulated calculation reveal the synergistic ORR catalysis of four- and five- coordinated Fe atoms in these samples. This work provides a new insight into the synthesis and application of metal-organic complex for metal single-atom catalysis.