China has the largest quantity of technically recoverable shale gas resources in the world. However, the complex, three-dimensional (3D), multi-scale structure of the shale reservoir makes it extremely challenging to fully understand the mechanisms that govern shale gas migration and recovery efficiency. In this study, focused ion beam-scanning electron microscopy (FIB-SEM) was applied to identify the nano- and micron-scale 3D structures, including inter-particle pores, organic matter pores, intra-particle pores and fractures, of shale sampled from the Longmaxi Formation, Sichuan Basin, China. The 3D structural and physical characteristics, such as morphology, porosity, connectivity, and permeability of multi-scale pores and fractures, were analysed using 3D reconstruction techniques and the lattice Boltzmann method (LBM). The results show that the majority of pores in the Longmaxi shale samples varied between 10 and 40 nm in size, although some significantly larger intra-particle pores were also detected. The micro-fractures exhibited higher permeability and gas migration capacity than adjacent nano-pores, and organic matter nano-pores displayed high porosity and good connectivity. This study provides a way to quantitatively characterise the multi-scale structure and its effect on shale gas migration and fracturing potential in the Longmaxi formation, as well as in similar shale reservoirs elsewhere around the world.