In recent years, porous materials containing micro- and nano-scale pores have found widespread applications. As the pore size decreases in such materials, rarefaction effects become significant in the pore flow, making the study of flow characteristics under higher Knudsen number conditions particularly crucial. In this work, through a direct simulation Monte Carlo (DSMC) method, an in-depth investigation is conducted into the gas flow characteristics and Klinkenberg effect in porous media with pore sizes ranging from 1 nm to 50 μm and Knudsen numbers spanning from 0.02 (slip flow) to 1200 (free molecular flow). The feasibility of using the DSMC method to simulate an internal free molecular flow in a porous medium under extreme rarefaction conditions with a Knudsen number of 1200 is validated. Furthermore, the impact of the gas pressure and porous medium pore size on the permeability is examined. The results reveal that with an increase in the Knudsen number, the dominant forces in the flow field transition from viscous forces to Knudsen diffusion, leading to a gradual increase in permeability. A comparative analysis reveals that existing apparent permeability models only provide satisfactory descriptions under certain Knudsen number conditions. Re-fitting the coefficient of the Kawagoe model and incorporating viscosity corrections leads to an apparent permeability model that can provide good predictions over a broader range of Knudsen numbers.