Characterization of soil functional pore structure is an essential prerequisite to understand key gas transport processes in variably saturated soils in relation to soil ecosystems, climate, and environmental services. In this study, the water-induced linear reduction (WLR) soil gas diffusivity model originally developed for sieved, repacked soil was extended to two simple, linear regions to characterize gas diffusion and functional pore-network structure also in intact, structured soil systems. Based on the measurements in soils with markedly different pore regions, we showed that the two linear regions can denote a percolation threshold where soil gas diffusion ceases due to interconnected water films, preferential gas diffusion in fracture networks (e.g., fractured limestone), and intra-aggregate or intramatrix gas diffusion. From measured or three-region WLR (3WLR) modeled gas diffusivity, we derived a simple pore connectivity index, Cip (ranging from 0 to 1), that showed a linear behavior with air-filled porosity (ε) for sieved, repacked soils ranging from 6 to 54% clay. We suggest that deviation from this Cip‒ε line is a direct measure of soil structure. The new 3WLR model could accurately describe gas diffusivity from moist to dry conditions across differently structured porous media, including narrow soil size fractions, perforated plastic blocks, fractured limestone, peaty soils, aggregated volcanic ash soils, and particulate substrates for Earth- or space-based applications. The new Cip function provided distinct soil structural fingerprints from moist to dry conditions for all porous media. We further used the 3WLR and Cip analyses to discuss the decreasing trend in gas diffusion percolation threshold with soil compaction.