The pore structure of shales, including pore morphology, connectivity, pore volume, specific surface area (SSA), and pore size distribution (PSD), is a significant factor in controlling gas storage and transport and the migration mechanisms of hydrocarbons. However, the lack of comprehensive characterization for both accessible and inaccessible pore structure increases the difficulty of gas-in-place estimation and gas exploration. In order to investigate the nanoscale pore system, integration of high-pressure mercury intrusion porosimetry (MIP), low-pressure N2/CO2 adsorption (LNA/LCA), and small-angle neutron scattering (SANS) were employed to obtain a multi-scale quantitative characterization of the nanopore structure of organic-rich marine shale samples from the Longmaxi and Niutitang Formations in China. PSDs obtained from the combined techniques appropriately cover an overall nanopore size range of shale (0.35–15,000 nm) and overcome the limits of the individual method. Uni-, bi, and multi-modal PSDs were observed, but the sizes of a significant portion of the nanopores observed in these shales range from 0.35 to 100 nm. Pore volumes and surface areas of micropores (<2 nm), mesopores (2–50 nm), and macropores (>50 nm) were characterized based on the best performance window of each technique: LCA for micropores; LNA and SANS for mesopores; and MIP for macropores. It was found that micropores are the major contributor to the total SSA for both the Longmaxi and Niutitang shales. With respect to pore volume, however, the contribution to the total pore volume has a trend of micropore < mesopore < macropore for the Longmaxi shale samples, but micro-/mesopore volumes are greater than macropore volumes for samples of the Niutitang shale. Strong correlations were also observed between total organic carbon (TOC) content and micropore volume and surface area, which implies that organic matter is a controlling factor in the micropore system of organic-rich shales. In addition, strong correlations between methane adsorption capacity and both micro-/mesopore volumes and SSAs indicate that micro-/mesopores are governing factors for methane storage. Furthermore, the fractions of accessible mesopore volume and surface area were quantitatively estimated by SANS and LNA. Correlation analyses suggest that the accessibility of the mesopore surface area could be an indicator for gas transport and storage in mesopores in organic matter. Thus, a shale with higher connectivity could have higher gas diffusion capability but lower gas adsorption capacity, and vice versa.