A multi-physical multi-scale CFD was developed for analyzing POX of methane (CH4) over a SSEP catalyst in a fixed-bed reformer. The model incorporates a conventional transport processes, heat transfer, and kinetics for POX of CH4 over the active components and the electrochemical processes occurring in the unique microstructure. The simulation results show that the temperature in the first reactor with the Ni based conventional catalyst is generally about 30 K lower than that in the second reactor with the Ni-based SSEP catalyst. This temperature difference is impossible to explain the huge difference in the conversion in these two reactors. The simulation results are compared with the experimental results. The good agreement can only be achieved by correctly describing the electrochemical processes and electrochemical promotion in the theoretical system. The validated model was used to predict the performance of the SSEP catalysts as a function of flow rate, O/C ratio, and the microstructure of the catalysts providing guidance for further optimization the SSEP catalyst.