Methanol autothermal reforming is a potential way to produce hydrogen that can be used for vehicle power batteries like PEMFC. Combining a reformer with a combustor to produce substantial hydrogen is promising, but the challenge of heat transfer efficiency between the reformer and combustor must be considered. Furthermore, the complexity of the system structure is not conducive to its large-scale operation level. In this paper, a novel methanol autothermal reforming hydrogen production system without catalytic combustion was built and developed, aiming to produce hydrogen-rich gas with low CO concentration. Process simulation and thermodynamic optimization on the target system were detailedly performed using Aspen Plus software and parameter sensitivity analysis methods. In addition, a methanol autothermal reforming hydrogen production system using catalytic combustion was taken as the reference system. The results indicated that the novel system could achieve a self-sustaining operation by the coupled methanol partial oxidation and steam reforming. And the product gas contained very low CO concentration (<10 ppm) due to the combined effects of water-gas shifting and CO preferential oxidation reactions. It was verified that under the maximal exergy efficiency condition, the exergy efficiency of the novel system is not significantly improved compared with the reference system, but the hydrogen yield is increased by about 27.65%, the thermal efficiency is increased by about 17.51%, and the exergy loss when generating unit molar H2 is reduced by 20.53 kJ/mol; Under the condition of maximum hydrogen yield, the indicators of the novel system also perform better. Notably, the reformer is the main exergy loss source in the novel system, which provides a theoretical basis for further optimization of parameter configuration. This work will be beneficial to researchers who study the miniaturization design of the integrated system of methanol hydrogen production coupled vehicle power battery.