The micro fabrication technology has facilitated the development of micro fuel processing systems to provide hydrogen for portable fuel cells. Methanol is a suitable liquid fuel for its high energy intensity and low operating temperature. In this study, a dynamic model for an integrated methanol micro fuel processing system and fuel cell is developed. The micro fuel processor employs plate-type micro devices. The steady state simulation analysis identifies the significant operating conditions for the micro FP/FC process, which are the feed flow rate and steam/carbon ratio of the steam reformer and the feed flow rate of the combustor. The dynamic simulation analysis compares the responds for the voltage change demand of PEMFC of three proposed control schemes, including the structures using double feedforward with double feedback control loops (CS1), double feedforward with single feedback control loops (CS2) and single feedforward with single feedback control loops (CS3). The CS2 plus a lag of 30 s is the best control structure.