As a national shale-gas demonstration zone in China, the Zhaotong area has great gas resource potential. However, the nanopore structure characteristics, methane adsorption capacity, and their affecting factors of the Lower Silurian Longmaxi Shale in this area remain unclear. To address these puzzles, we conducted a series of experiments, such as X-ray diffraction, field emission scanning electron microscopy, low-pressure adsorption, and high-pressure methane adsorption, and we calculated the relevant characteristic parameters, such as pore volume (PV), specific surface area (SSA), fractal dimension, and Langmuir parameters by using the nonlocal density functional theory method, Frenkel-Halsey-Hill theory, and Langmuir model, respectively. The results indicate that the nanopores of the Lower Longmaxi Shale in the Zhaotong area are composed of micropores and mesopores, which mainly exist as organic matter (OM) pores. The pore surface exhibits a high degree of heterogeneity as indicated by the fractal dimensions ranging from 2.845 to 2.866. The nanopore structure characteristics (i.e., SSA and PV) and methane adsorption capacity are mainly controlled by the total organic carbon (TOC) content. In addition, the mineralogical composition (i.e., the quartz and clay content) also contributes significantly to the micropore PV and gas content. The external provenance has a significant effect on the mineralogical composition, TOC content, and methane adsorption capacity. With the increasing influence of the external provenance, the biogenic quartz content decreases and the relationship between the quartz content and TOC content becomes more discrete, which indicates the change of depositional environment, and the clay content increases, which can dilute the OM concentration during the deposition and enhance the compaction potential, and it can eventually result in less gas content. The results of this study reveal the nanopore system characteristics of the Longmaxi Shale in the Zhaotong area and provide further insight into the influence of external provenance on reservoir characteristics and gas content variability of the Lower Longmaxi Shale in the southern Sichuan Basin.