Microbial fuel cell (MFC) is a renewable bio-electrochemical technology which can harvest bioelectricity from wastewater treatment using exoelectrogenic bacteria. The development of nonprecious metal catalysts for enhancing the oxygen reduction reaction (ORR) based on abundancy is important for MFC. Herein, a rose flower-like nitrogen-doped NiCo2O4/carbon (N-NiCo2O4/C) has been prepared via a facile hydrothermal method and is utilized as an effective cathode electrocatalyst in air cathode MFC. N-NiCo2O4/C has many active sites within the rose flower structure resulting in a power density of 1249.86 mW m−3, which is slightly lower than that of Pt/C (1322.71 mW m−3), and only has a decrease of 2.71% after 50-cycle operation in air cathode MFC. The electrochemical evaluations suggest that the main ORR pathway for N-NiCo2O4/C is a four-electron reduction of oxygen because the synergistic effect among Ni, Co and different N-species (Oxidized-N, Graphitic-N, Pyrrolic-N and Pyridinic-N) contributes to the ORR activity. This work indicates that rose flower-like N-NiCo2O4/C is an efficient functional catalyst presenting an alternative to the costly Pt/C in air cathode MFC.