A high temperature proton exchange membrane fuel cell system integrated with a methanol steam reformer is developed in this study. A system model considering thermal-coupled balance-of-plant components and several temperature constraints is established. The hydrogen production performance of the reformer is evaluated and experimentally validated. A high methanol conversion rate above 90.1% with a low CO content below 1.5% are obtained with the reformer temperature of 573 K at a steam to carbon ratio of 1.3. Besides, CO poisoning effect on the stack is inhibited with an increase in the operating temperature. The fuel cell voltage increases 35% with variation of the operating temperature from 160 °C to 180 °C at the current density of 0.4 A/cm2 and CO molar ratio of 1%. Furthermore, model-based analysis is conducted to investigate impacts of various input parameters on system operating performance. The proposed system presents a maximum electrical efficiency of 37.8%, and increasing the current density and decreasing air excess ratio are favorable for improving the net power output, but also increasing the heat duties of components and resulting in a reduced safety operating region. Finally, an optimal operating strategy with maximum system efficiency is proposed for variable output powers ranging from 15 to 55 W.