A key target of shale gas exploration and production in China is the organic-rich black shale of the Wufeng Formation-Longmaxi Formation in the Sichuan Basin and its periphery. The set of black shale contains abundant graptolites, which are mainly preserved as flattened rhabdosomes with carbonized periderms, is an important organic component of the shale. However, few previous studies had focused on the organic matter (OM) which is derived from graptolite and its pore structure. In particular, the contributions of graptolites to gas generation, storage, and flow have not yet been examined. In this study, focused ion beam-scanning electron microscope (FIB-SEM) was used to investigate the characteristics of the graptolite-derived OM and the micro-nanopores of graptolite periderms. The results suggested that the proportion of OM in the graptolite was between 19.7% and 30.2%, and between 8.9% and 14.4% in the surrounding rock. The total organic carbon (TOC) content of the graptolite was found to be higher than that of the surrounding rock, which indicated that the graptolite played a significant role in the dispersed organic matter. Four types of pores were developed in the graptolite periderm, including organic gas pores, pyrite moulage pores, authigenic quartz moldic pores, and micro-fractures. These well-developed micro-nano pores and fractures had formed an interconnected system within the graptolites which provided storage spaces for shale gas. The stacked layers and large accumulation of graptolites resulted in lamellation fractures openning easily, and provided effective pathways for the gas flow. A few nanoscale gas pores were observed in the graptolite-derived OM, with surface porosity lie in 1.5%–2.4%, and pore diameters of 5–20 nm. The sapropel detritus was determined to be rich in nanometer-sized pores with surface porosity of 3.1%–6.2%, and pore diameters of 20–80 nm. Due to the small amount of hydrocarbon generation of the graptolite, supporting the overlying pressure was difficult, which caused the pores to become compacted or collapsed.