Volcanic rock reservoirs for oil and gas are known worldwide for their considerable heterogeneity. Micropores and fractures play vital roles in the storage and transportation of natural gas. Samples from volcanic reservoirs in Songliao Basin, CS1 and W21, belonging to the Changling fault depression and the Wangfu fault depression, respectively, have similar lithology. This study employs micro–nano CT scanning technology to systematically identify the key parameters and transport capacities of natural gas within volcanic reservoirs. Using Avizo 2020.1software, a 3D digital representation of rock core was reconstructed to model pore distribution, connectivity, pore–throat networks, and fractures. These models are then analyzed to evaluate pore/throat structures and fractures alongside microscopic parameters. The relationship between micropore–throat structure parameters and permeability was investigated by microscale gas flow simulations and Pearson correlation analyses. The results showed that the CS1 sample significantly exceeded the W21 sample in terms of pore connectivity and permeability, with connected pore volume, throat count, and specific surface area being more than double that of the W21 sample. Pore–throat parameters are decisive for natural gas storage and transport. Additionally, based on seepage simulation and the pore–throat model, the specific influence of pore–throat structure parameters on permeability in volcanic reservoirs was quantified. In areas with well–developed fractures, gas seepage pathways mainly follow fractures, significantly improving gas flow efficiency. In areas with fewer fractures, throat radius has the most significant impact on permeability, followed by pore radius and throat length.