Gas flow in soil plays a crucial role in terrestrial ecosystems, and numerical simulation of their movement needs to know their effective diffusion coefficients. How pore structure influences the effective diffusion coefficient has been studied intensively for dry porous media, but much remains unknown for unsaturated soils. Here, we employed the X-ray tomography technique at the pore scale to directly obtain the soil structures, the geometry of their pores and the water distribution under different water saturation levels were calculated using a morphological model. The results show that pore structures including porosity, interface area of gas–solid–water and pore diameter are closely related to water saturation. The increase of mean pore diameter with gas saturation can be fitted into a power law. We also investigated the impact of pore geometry and water saturation on the effective diffusion coefficients, which is independent of the molecular mass of gas after normalization. As the normalized effective Knudsen diffusion coefficient increases with average pore diameter following a power law, with the scaling factor related to pore geometry and the exponent is a constant, we explained and proved that the Knudsen diffusion coefficient increases with gas saturation, also following a power law.