This study aims to explore the reservoir characteristics and formation mechanisms of ultra-deep shale gas in the Ordovician–Silurian Wufeng–Longmaxi Formation in the Sichuan Basin in order to provide theoretical support and practical guidance for the exploration and development of ultra-deep shale gas. With recent breakthroughs in ultra-deep shale gas exploration, understanding its organic matter development, mineral composition, and reservoir space characteristics has become particularly important. The background of this research lies in the significant potential of ultra-deep shale gas, which remains inadequately understood, necessitating an in-depth analysis of its pore structure and reservoir quality. Through a systematic study of the ultra-deep shale in well FS1 of Sichuan Basin, that the following was found: (i) The ultra-deep shale in the Wufeng–Longmaxi Formation is mainly composed of quartz and clay minerals, exhibiting high total organic carbon (TOC) and high porosity characteristics, indicating it is in an overmature thermal evolution stage. (ii) Organic pores and microcracks in the ultra-deep shale are more developed compared to middle-shallow and deep shale, forming a complex pore structure that is conducive to gas storage. (iii) In the diagenesis process, the dissolution and recrystallization of the biogenic skeleton promote the cementation between autogenetic quartz particles, forming a rigid skeleton that effectively inhibits the impact of mechanical compaction. (iv) The overpressure environment created by the hydrocarbon generation process, along with gas production from hydrocarbon cracking, can effectively offset the mechanical compaction of overburden pressure on micropores, and this overpressure environment also promotes the further development of microfractures, which is beneficial for the development and preservation of ultra-deep shale pores. In summary, this study not only reveals the reservoir characteristics and formation mechanisms of ultra-deep shale but also provides essential references for the exploration and development of ultra-deep shale gas in the Sichuan Basin and similar regions, emphasizing the ongoing significance of research in this field.