In a typical integration of the micro-channel fuel processor, the thermal imbalance and the volume inefficiency have significant negative effect on both catalyst life-time and system performance. Therefore the optimal compact design concerning heat transfer is of great importance to achieve the possible system miniaturization by favorable thermal balance and catalyst loading reduction. This paper represents the comprehensive computational modeling efforts on the conjugate heat and mass transport in micro-channel fuel processor, particularly the methanol stream reforming section for a compact portable system. A two-dimensional numerical modeling for a micro-channel coated by catalyst Cu/ZnO/Al2O3 on the inner walls is introduced for in-depth analysis of the heat and mass transport phenomena based on the surface kinetics and catalytic process. The reactor was subjected to operate at atmospheric pressure condition and in a temperature range of 160oC to 260oC. In the model, water gas shift reaction and decomposition reaction were assumed to be at equilibrium. A kinetic model was developed and then computational results were compared with the experimental data available in the literature. The results were successfully applied to geometry optimization in reaction flow channel, fuel conversion efficiency and catalyst loading. Finally the case study was carried out by considering the key parameters, i.e. temperature, W/F ratio and steam to carbon ratio.