Microbial fuel cells (MFCs) as a renewable energy conversion technology have been attracting increasing attention in the past decades. However, a deeper understanding of bioelectrochemical reaction in electrodes is urgent to improve the cell performance towards practical applications. In this paper, a mathematical model of air cathode MFCs was proposed by coupling mass transport and charge conservation with bioelectrochemical/electrochemical reactions. The model was validated based on experimental results and further used to predict the performance of MFCs. The effect of mass transport including oxygen and substrate on electrode kinetics was studied based on the model. The results showed that enhancing mass transport in both anode and cathode remarkably facilitated the electrode current and hence the cell performance, and oxygen transfer in catalyst layer of cathode is the dominating factor limiting the cell performance. The proposed model can provide a facile avenue to capture the interdependence of electrode variables and help guide electrode design for optimizing the performance of MFCs in practical applications.