The pressure-driven gas transport characteristics through a porous medium consisting of arrays of discrete elements is investigated by using the direct simulation Monte Carlo (DSMC) method. Different porous structures are considered, accounting for both two-and three-dimensional arrangements of basic microscale and nanoscale elements. The pore scale flow patterns in the porous medium are obtained, and the Knudsen diffusion in the pores is studied in detail for slip and transition flow regimes. A new effective pore size of the porous medium is defined, which is a function of the porosity, the tortuosity, the contraction factor, and the intrinsic permeability of the porous medium. It is found that the Klinkenberg effect in different porous structures can be fully described by the Knudsen number characterized by the effective pore size. The accuracies of some widely used Klinkenberg correlations are evaluated by the present DSMC results. It is also found that the available correlations for apparent permeability, most of which are derived from simple pipe or channel flows, can still be applicative for more complex porous media flows, by using the effective pore size defined in this study.