The development microbial fuel cell relies heavily on cathodic catalysts to provide excellent activity and fast electron rotor transfer rates. However, the design of such electrocatalysts is extremely challenging. Here, a strategy is proposed to regulate the electrocatalyst comprised of cobalt and manganese oxides embedded the porous nitrogen-doped carbon (Co3O4-MnO2/NC) with dominant crystal surface by geometric and electronic engineering. Experimental results and theoretical calculations show that the coordination of bimetallic oxides with N atoms induces an asymmetric distribution of charge of central metal sites, which promotes the adsorption/desorption of oxygen intermediates. This electrocatalyst exhibits excellent oxygen reduction reaction (ORR) activity, long-term stability and antitoxic tolerance. Importantly, microbial fuel cell equipped with Co3O4-MnO2/NC generates excellent performance in power density, chemical oxygen demand (COD) removal rate and coulomb efficiency. This work demonstrates the importance of geometric and electronic engineering design of bimetallic oxide to expose more dominant crystal faces to improve electrocatalytic activity in electrochemical energy conversion systems.