Technological advances in horizontal drilling and hydraulic fracturing have paved the way for the exploration and production of shale gas and shale oil, the fastest growing energy sector globally. The imaging and quantification of the geometry, sizes, network and distribution of extremely fine-grain minerals, organic matter and pores are a significant component for the macroscopic and microscopic characterisation of shale reservoirs but is also highly challenging. X-ray computed tomography (XCT) combined with 3D Electron Microscopy (EM) are used to address this challenge and give us information in 3D from multiple length scales over 3 orders of magnitudes: mesoscale (R1), microscale (R2), submicron-scale (R3), low-resolution nanoscale (R4) and high-resolution nanoscale (R5) with spatial resolutions of ~10micro metre, ~1micro metre, ~130 nm, ~50nm and ~5nm, respectively.The multi-scale imaging and quantification method was initially applied here to the Carboniferous Bowland Shale, the largest potential shale gas play in the UK. The appropriate length scales (both field of view and voxel size) of specified phases such as pores, organic matter, clay minerals and non-clay minerals were analysed. The low connectivity of pores and high connectivity of organic matter suggests that the 20 nm and larger pores imaged did not form connected flow paths, demonstrating that porous gas flow through this sample cannot be the main transport mechanism and diffusive transport through the organic matter and clay minerals must also be considered. Then, the variation of organic matter and pore distribution along a TOC gradient were analysis on Lublin gas-mature shale samples in Poland and Baltic oil-mature shale samples in Lithuania. The results show intergranular pores dominated in this series of samples, including organic interface pores and inter-mineral pores, which further confirm that organic matter is not the primary influencing factor for porosity, but the clay minerals. Finally, a novel multi-stage workflow of pore system is proposed relying on both image quantification and numerical modelling of geological features with studies in Jurassic Haynesville shale in the US. Three stages are divided according to pore variation, mineral variation and microfacies variation across four distinct length scales (R1-R4/R5), and permeability was simulated based on the upscaled pore system. The final computed porosity and permeability shows acceptable errors when compared with the helium porosity and press decay permeability. Beyond the lab measurements, the pore occurrence and size distribution were computed in the upscaling process.The combining of XCT and 3D-EM provides a powerful tool for the multi-scale imaging and quantification of microstructural information in shales, allowing the visualization of pores, organic matter and inorganic mineral phases over a range of scales over three orders of magnitude (~ 10 micro metre to ~ 5 nm), and the volume fraction of each phases shows a reasonable correlation to traditional physical and chemistry quantification data. The further studies, such as the variation of organic matter and pores, upscaling of porosity and permeability presented in this study, has verified the feasibility of the proposed multi-scale method and promises a bit potential for reservoir prediction and other challenges in geological studies.