The rational development of high-performance anode and cathode electrodes for microbial fuel cells (MFCs) is crucial for enhancing MFC performance. However, complex synthesis methods and single-performance electrode materials hinder their large-scale implementation. Here, three-dimensional hierarchical porous (3DHP) Fe3O4/Fe-N-C composites were prepared via the hard template method. Notably, Fe3O4/Fe-N-C-0.04-600 demonstrated uniformly dispersed Fe3O4 nanoparticles and abundant Fe-Nx and pyridinic nitrogen, showing excellent catalytic performance for oxygen reduction reaction (ORR) with a half-wave potential (E1/2) of 0.74 V (vs. RHE), surpassing Pt/C (0.66 V vs. RHE). Moreover, Fe3O4/Fe-N-C-0.04-600 demonstrated favorable biocompatibility as an anode material, enhancing anode biomass and extracellular electron transfer efficiency. Sequencing results confirmed its promotion of electrophilic microorganisms in the anode biofilm. MFCs employing Fe3O4/Fe-N-C-0.04-600 as both anode and cathode materials achieved a maximum power density of 831.8 ± 27.7 mW m−2, enduring operation for 38 days. This study presents a novel approach for rational MFC design, emphasizing bifunctional materials capable of serving as anode materials for microorganism growth and as cathode catalysts for ORR catalysis.