This paper presents a methodology for understanding the phenomena that occur inside an actual electrode in a flow battery. We reconstruct the 3D microstructure of an electrode based on the real microstructure morphology to model the effect of mesopores on the electrodes electrochemical performance. In various reconstructed electrode structures, the presence of mesopores on carbon fibers has been shown to improve the performance compared to an electrode with no pores on the carbon fibers. This provides valuable insight for the preparation of a carbon electrode for a flow battery. In other words, the activity of carbon fibers with mesopores should be considered when preparing carbon paper, which will probably significantly improve the electrode performance. In addition, unlike the homogenous models in previous reports, simulation results showed the electrolyte flow and current density distribution in the pores and gap bridging pores. The pore interconnectivity and accessibility could be determined, which will provide significant guidance for electrode preparation to guarantee the utilization of a specific surface area. The approach proposed in this work sheds light on the phenomena inside the microstructure and provides detailed geometries for building the relationship between the structure and performance.