The growing demand for energy and environmental concerns make finding economical and environmentally sustainable solutions for the effective and more utilization of natural gas, as the cleanest fossil fuel, imperative. Among different approaches to reach this goal, chemical conversion is of great interest. Future energy carriers such as hydrogen and methanol can be produced by the natural gas conversion. Recently, the auto-thermal methanol synthesis (AMS) process has become an important alternative for natural gas conversion and monetization. Concerning the equilibrium limitation of methanol synthesis reactions, there are two different configurations for membrane reactor, which may be used in this process. In the first configuration (in situ H2 addition configuration), the Pd/Ag membrane was applied while in the other one (in situ H2O removal configuration) H-SOD membrane was used. Generally, the proposed reactor is composed of three concentric tubes of which the inner tube is separated by a membrane from second one (exothermic side). A steady-state heterogeneous model was developed to investigate the possibility of improving AMS performance by means of two different membranes. The proposed model has been used to compare the performance of two different auto-thermal configurations with respect to the non-membrane one under identical process conditions. It was found that the reactor in the in situ water removal configuration operates with higher methanol yield, higher carbon dioxide removal which causes a lower environmental impact and longer exothermic catalyst life as a result of the more favourable temperature profile as well as reducing H2O promoted catalyst deactivation. However, thermal efficiency of reactions is declined and the dehydrogenation reaction yield in both configurations is not significantly different. Finally, the influence of inlet temperature of sweep gas as one of the key operating variables is investigated on products yield. The results suggest