The distribution of multiscale pores and fractures in coal and rock is an important basis for reflecting the capacity of fluid flow in coal seam seepage passages. Accurate extraction and qualitative and quantitative analysis of pore-fracture structures are helpful in revealing the flow characteristics of fluid in seepage channels. The relationship between pore and fracture connectivity can provide a scientific reference for optimizing coal seam water injection parameters. Therefore, to analyse the change in permeability caused by the variability in the coal pore-fracture network structure, a CT scanning technique was used to scan coal samples from the Leijia District, Fuxin. A total of 720 sets of original images were collected, a median filter was used to filter out the noise in the obtained images, and to form the basis of a model, the reconstruction and analysis of the three-dimensional pore-fracture morphology of coal samples were carried out. A pore-fracture network model of the coal body was extracted at different scales. Using the maximum sphere algorithm combined with the coordination number, the effect of different quantitative relationships between pore size and pore throat channel permeability was studied. Avizo software was used to simulate the flow path of fluid in the seepage channels. The change trend of the fluid velocity between different seepage channels was discussed. The results of the pore-fracture network models at different scales show that the pore-fracture structure is nonuniform and vertically connected, and the pores are connected at connecting points. The pore size distribution ranges from 104 μm to 9425 μm. The pore throat channel length distribution ranges from 4206 μm to 48073 μm. The size of the coordination number determines the connectivity and thus the porosity of the coal seam. The more connected pore channels there are, the larger the pore diameters and the stronger the percolation ability. During flow in the seepage channels of the coal, the velocity range is divided into a low-speed region, medium-speed region and high-speed region. The fluid seepage in the coal seam is driven by the following factors: pore connectivity > pore and pore throat dimensions > pore and pore throat structure distribution. Ultimately, the pore radius and pore connectivity directly affect the permeability of the coal seam.