Traditional research on apparent permeability in shale reservoirs has mainly focussed on effects such as poromechanics and porosity-assisted adsorption layers. However, for a more realistic representation of field conditions, a comprehensive multi-scale and multi-flowing mechanism model, considering the fracturing process, has not been thoroughly explored. To address this research gap, this study introduces an innovative workflow for dynamic permeability assessment. Initially, an accurate description of the pore size distribution (PSD) within three major mineral types in shale is developed using focussed ion beam-scanning electron microscopy (FIB-SEM) and nuclear magnetic resonance (NMR) data. Subsequently, an apparent permeability model is established by combining the PSD data, leading to the derivation of dynamic permeability. Finally, the PSD-related dynamic permeability model is refined by incorporating the effects of imbibition resulting from the fracturing process preceding shale gas production. The developed dynamic permeability model varies with pore and fracture pressures in the shale reservoir. The fracturing process induces water blockage, water-film formation, and water-bridging phenomena in shale, requiring additional pressure inputs to counteract capillary effects in hydrophilic minerals in shale, But also increases the overall permeability from increasing permeability at larger scale pores. Unlike traditional reservoirs, the production process commences when the fracture is depleted to 1–2 MPa exceeds the pore pressure, facilitated by the high concentration of hydrophobic organic matter pores in shale, this phenomenon explains the gas production at the intial production stage. The reduction in adsorption-layer thickness resulting from fracturing impacts permeability on a nano-scale by diminishing surface diffusion and the corresponding slip flow of gas. this phenomenon increases viscous-flow permeability from enlarged flow spacing, but the increased viscous flow does not fully offset the reduction caused by adsorbed-gas diffusion and slip flow. In addition to the phenomena arising from various field conditions, PSD in shale emerges as a crucial factor in determining dynamic permeability. Furthermore, considering the same PSD in shale, under identical pore spacing, the shape factor of slit-like clay minerals significantly influences overall permeability characteristics, much more slit-shaped pores(higher shape factor) reduce the overall permeability. The dynamic permeability-assisted embedded discrete fracture model (EDFM) showed higher accuracy in predicting shale gas production compared to the original model.