In this study, a thermodynamic analysis of the low temperature autothermal reforming (ATR) of dimethyl ether (DME) for hydrogen production was conducted. The Pd/Zn/γ-Al2O3 catalyst coated on the honeycomb cordierite ceramic was applied to catalyze the reaction, and the optimum activity temperature of this catalyst was demonstrated experimentally and through simulations to be 400 °C. Furthermore, an optimal model predictive control (MPC) strategy was designed to control the hydrogen production rate and the catalyst temperature. Experimental and simulation results indicated that the controller was automated and continuously reliable in the hydrogen production system. By establishing the state-space equations of the autothermal reformer, it can precisely control the feed rates of DME, high-purity air and deionized water. Ultimately, the hydrogen production rate can be precisely controlled when the demand curve changed from 0.09 to 0.23 mol/min, while the catalyst temperature was maintained at 400 °C, with a temporary fluctuation of 4 °C during variations of the hydrogen production rate. Therefore, the tracking performance of the hydrogen production and the anti-disturbance were satisfactory.