Permeability estimation has been extensively researched in diverse fields; however, methods that suitably consider varying geometries and changes within the flow region, for example, hydraulic fracture closing for several years, are yet to be developed. Therefore, in the present study a new permeability estimation method is presented based on the generalized Darcy’s friction flow relation, in particular, by examining frictional flow parameters and characteristics of their variations. For this examination, computational fluid dynamics (CFD) simulations of simple hydraulic fractures filled with five layers of structured microbeads and accompanied by geometry changes and flow transitions are performed. Consequently, it was checked whether the main structures and shapes of each flow path are preserved, even for geometry variations within porous media. However, the scarcity and discontinuity of streamlines increase dramatically in the transient- and turbulent-flow regions. The quantitative and analytic examinations of the frictional flow features were also performed. Accordingly, the modified frictional flow parameters were successfully presented as similarity parameters of porous flows. In conclusion, the generalized Darcy’s friction flow relation and friction equivalent permeability (FEP) equation were both modified using the similarity parameters. For verification, the FEP values of the other aperture models were estimated and then it was checked whether they agreed well with the original permeability values. Ultimately, the proposed and verified method is expected to efficiently estimate permeability variations in porous media with changing geometric factors and flow regions, including such instances as hydraulic fracture closings.