The membrane separation process has been developed as an effective and efficient method for obtaining ultra-high purity hydrogen from impure feed streams. A typical membrane gas flow possesses multi-scale flow characteristics, comprising a macroscopic flow regime on both sides of the membrane and a microscopic flow regime in the pores within the membrane. A better understanding of the fundamentals of such flow behaviors and mass transfer at a multi-scale level is therefore crucial for a better membrane architecture design, which could lead to better membrane separation efficiency and reliability for hydrogen productions in fuel cells. In this paper, a novel numerical analysis method combining the direct simulation Monte Carlo (DSMC) method with the smoothed particle hydrodynamics (SPH) method is presented for the multi-scale flow prediction in a membrane. Using the coupled method, the rarefied flow behaviors within a micro-orifice pore can be predicted by the DSMC method, while the continuum flow behaviors on both sides of the membrane can be simulated by the SPH method simultaneously. To investigate the various flow behaviors and mass transfer between different components, such as H-2 and CO in the membrane, the pressure, velocity, molar concentration, mass flowrate and rarefaction of the H-2 and CO components are compared in details. The influences to the multi-scale flow from the orifice feature and size are discussed. Some unique phenomena are observed to be quite different from that observed in either a solely macroscopic or microscopic flow. The results can be greatly beneficial for the understanding of the mechanism of membrane separation, and the designing of the membranes for hydrogen productions in fuel cell applications. Copyright (C) 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.