Microstructures and pore systems in shales are key to understanding the role of shale in many energy applications. This study proposes a novel multi-stage upscaling procedure to comprehensively investigate the heterogeneous and complex microstructures and pore systems in a laminated and micro fractured shale, utilising 3D multi-scale imaging data. Five imaging techniques were used for characterisation from sub-nanoscale to macroscale (core-scale), spanning four orders of magnitude. Image data collected using X-ray tomography, Focused Ion Beam, and Electron Tomography techniques range in voxel size from 0.6 nm to 13 mu m. Prior to upscaling, a novel two-step analysis was performed to ensure sub-samples were representative. Following this, a three-step procedure, based on homogenising descriptors and computed volume coefficients, was used to upscale the quantified microstructure and pore system. At the highest resolution (nanoscale), four distinct pore types were identified. At the sub-micron scale equations were derived for three pore-associated phases. At the microscale, the volume coefficients were recalculated to upscale the pore system to the millimetre- scale. The accuracy of the upscaling methodology was verified, predicting the total porosity within 7.2% discrepancy. The results provide a unique perspective to understand heterogeneous rock types, breaking though prior scale limitations in the pore system. (C) 2019 Published by Elsevier Ltd.