The nanometer-scale architecture of organic matter (OM) and associated pores in highly mature gas shales from the lower Silurian Longmaxi Formation in the upper Yangtze platform of south China were investigated using field emission scanning electron microscopy (SEM), focused ion beam SEM, and low-pressure gas (N2 and CO2) adsorption bulk pore characterization. The Longmaxi shale comprises fine-grained siliciclastic rocks deposited in a marine shelf environment, which was dominated by quartz and clay minerals. Four porous OM types were found in the Longmaxi shale on the basis of the chemical composition and spatial occurrence of OM, including (1) isolated original OM particles, (2) OM–clay mineral complexes, (3) OM–heavy mineral complexes, and (4) secondary migrated bituminous OM. The pores in the particulate OM are not homogeneously distributed, and the processes leading to different pores depend on the specific OM type. The nature of OM-hosted pores is a result of several factors, such as primary porous kerogen, mechanical compaction, organic–inorganic interactions, gaseous and liquid hydrocarbon generation, retention, and expulsion. Pore volumes and specific surface areas of the Longmaxi shale derived from low-pressure N2 and CO2 adsorption experiments reveal positive linear relationships with total organic carbon contents, which indicates that the pore systems in the highly mature Longmaxi shale are dominated by OM-hosted pores. Additionally, the OM-hosted pores appear connected compared to pores in the mineral matrix. Therefore, the OM-hosted pore systems offer the preferential storage space and primary migration pathways for natural gas in the Longmaxi shale reservoir.