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Characterizing nanopore structure is one of the most important factors in understanding gas storage and transport in shale reservoirs, but remains a significant challenge. In this work, we combine the benefits of Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) and Nuclear Magnetic Resonance Cryoporometry (NMR-C) to characterize the nanopore structure of lower Paleozoic shales from Chongqing, southwestern China. Mineral composition is qualified through X-ray Energy Dispersive Spectroscopy (EDS) and Field-Emission Scanning Electron Microscopy (FE-SEM). Voids in 2D micrographs are classified into types of meso- and/or microfractures, inter particle pores (InterP pores), intraparticle pores (IntraP pores), and pores in organic matter (OM pores). An Otsu thresholding algorithm and an edge detection algorithm (in Avizo) are used to segment OM, InterP, and IntraP pores and to establish 3D pore structure for pore-network modeling (PNM). The pore size distribution (PSD) is measured via PNM and compared to the PSD recovered from NMR-C. Results indicate that the small OM pores have favorable potential for storing adsorbed gas because of their apparent interconnectivity and higher porosity; conversely, InterP and IntraP pores are mostly isolated and with low porosity. The peaks of the PSD, recovered from PNM, are in the ranges 10–20 nm and 60–120 nm and are in good agreement with the peaks of the PSD recovered from NMR-C. This suggests that the NMR signals in these discontinuous ranges are due to OM, InterP, and IntraP pores. This indirectly demonstrates that the probe liquid in the NMR-C experiments (i.e., water) may indeed enter the nanoscale pores in the shale during centrifugal saturation. Comparison of the PSD from PNM and NMR-C also shows that NMR-C has a higher sensitivity and accuracy in detecting nanopores. Combining FIB-SEM and NMR-C is a promising technique in detecting and characterizing the nanoporosity of shales.