The microscopic pore structure is one of the most important factors to understand shale gas reservoirs. Recognized as a non-destructive method, nano-transmission X-ray microscopy (Nano-TXM) is sufficiently powerful to resolve nanometer pore structures and to quantify the effective network in shale. In this work, three dimensional (3D) pore networks of typical pore structures, such as organic matter pores (OM pores), interparticle pores (InterP pores), intraplatelet pores within clay aggregates (IntraP pores) and intercrystalline pores within pyrite (InterC pores), developing in Jiulaodong (JLD) formation shale in the Weiyuan 201 well (W201) in Sichuan Basin were reconstructed by Nano-TXM. Meanwhile, the pore morphology, pore size, porosity and interconnectivity were analyzed using Pore Network Modeling (PNM). The results indicated that the pore shape, pore size distribution, porosity and interconnectivity varied between the four pore types. Nanometer pores ranging from 150 nm to 1000 nm dominate the OM pores in the samples. However, pores with a sheet-like structure that are larger than 1000 nm are mainly found in InterP and IntraP pores. OM pores and InterP pores have larger porosities (35% and 23.7%, respectively) than the other two pore types. OM pores, InterP pores and InterC pores exhibit good and homogenous 3D connectivity, whereas IntraP pores have good extensity parallel to the clay mineral orientation but have no connectivity perpendicular to it. The 3D morphology and pore parameters suggest that the nano-pores in OM and InterC pores store absorbed gas and might be connected by micropores that existed in InterP and IntraP pores. The characterization of the pore structure in shale samples provides useful information for shale gas development. (C) 2015 Elsevier Ltd. All rights reserved.