Herein, we reported a two-dimensional, two-phase mass transport model for a flat-plate microbial fuel cell (MFC) by evoking a membrane phase and a solid phase that employed in direct methanol fuel cells. In the present proposed MFC modeling, the liquid phase and solid phase correspond to proton transfer and electron transfer, respectively. The model established by this method overcomes the problem that it is difficult to establish the relationship between cathode and anode through the internal relation of the MFC in previous models. Finally the proposed model was employed to investigate the distribution of the concentration of the chemical components in the MFC, the overpotential and the bio-electrochemical reaction rates in biofilm and cathode catalyst layer. This model can be used as a framework for other types of MFC and it is suitable for optimization of the structure and internal mechanisms. (C) 2016 Elsevier Ltd. All rights reserved.