Methanol steam reforming (MSR) has been used for in-situ hydrogen production, while hydrogen purification remains a technical challenge to limit the applications of using hydrogen for fuel cells. This study presents a pure hydrogen generation system (PHGS) by integrating MSR and hydrogen purification modules, this system enables low-temperature reforming and high-temperature purification to achieve high yield and recovery of hydrogen. To investigate the combined effects of feedstock flow rates and pressure on MSR and purification, the performance of each module and overall PHGS system were tested. The results showed that PHGS can stably produce high purity hydrogen (>99.99%) under different conditions, the synergistic effects of two modules lead to hydrogen yield exceeding the numerical sum of individual modules. At methanol feed rate of 1.00 g/min and system pressure of 5.0 bar, the pure hydrogen flow rate, CO content, pure hydrogen yield, hydrogen recovery and thermal power output were tested about 1.70 ± 0.01 L/min, 2.4 ± 0.1 ppm, 81.1 ± 0.5%, 87.6 ± 0.5% and 350 W. The PHGS can deliver up to 500 W of thermal power and is suitable for small range-extended electric vehicles. Our work on the developed PHGS can provide a significant reference for future practical applications of systems combining MSR and membrane purification.