The present study focuses on the mathematical description and control analysis of an integrated power system for hydrogen production via methanol autothermal reforming. The unit consists of the reformer reactor where methanol, air and water are co-fed to produce a hydrogen rich stream through a series of reactions. The ratios of the reactants are chosen in such a way, so that adiabatic conditions are achieved. The hydrogen main stream is fed to the preferential oxidation reactor (PROX) for the reduction of CO at acceptable levels (below 50ppm) with the use of additional air. Finally, the outlet of the PROX enters the anode of a PEM fuel cell where power production takes places to serve a constant or variable load unit. In the present study, the mathematical models of the basic subsystems will be developed. The operation of the two reactors is described by a combination of partial differential equations (mass and energy balances) and non-linear equations (kinetic expressions of the reactions), while the voltage-current (V-I) characteristic of the PEM fuel cell is a non-linear equation that depends however, on ordinary differential equations of the mass and energy balance in the PEM fuel cell. The results of the dynamic operation of all the subsystems in connection will be given and discussed. Furthermore, an insight on the challenging control scheme will be applied in order to identify possible ways of setting up a reliable and robust control structure based on the developed mathematical model.