Although pore-network characterization of shale rock systems is being actively investigated, a detailed understanding of the pore network at the nanometer-to-millimeter scale has not been completed. This is because of the technical limitations of collecting and integrating data at the wide spectrum of scales necessary to understand the pore network. Permeability for a micrometer-scale volume can be estimated based on pore-scale modeling for the focused ion beam/scanning electron microscope (FIB/SEM) milled 3D pore network; however, it is not clear how representative this permeability is for larger volumes. In this study, an integrated method employing FIB/SEM, helium ion microscopy, and synchrotron X-ray micro-computed tomography (micro-CT) was developed and applied to a Barnett Shale sample for pore and organic-matter distribution network characterization and upscaling. Organic-matter particle network characterization using synchrotron micro-CT scanning is the key step that bridges the gap between nanometer-scale and macroscopic observations. A conceptual model and an empirical equation were developed for permeability estimation based on FIB/SEM and micro-CT image analysis and mercury intrusion data. Upscaled permeability estimation was produced based on the empirical equation and parameters from the image and mercury intrusion analysis. The resulting permeability values of 2-22 and 0.6-3 nD for parallel and perpendicular to bedding planes, respectively, are comparable to laboratory measurements of the same sample. The proposed technique provides a method for more basic understanding of the pore network and pore-permeability relationship for organic-rich shale samples, and can serve as a basis for further upscaling to core and formation scale.