In the deep Longmaxi Formation shale gas reservoirs of the southern Sichuan Basin, strong overpressure is universally developed to varying degrees. However, there is currently a lack of in-depth research on the formation mechanisms, evolutionary patterns, and the controlling effects on reservoir pore characteristics of strong overpressure. This limitation significantly restricts the evaluation of deep shale gas reservoirs. This study selected typical overpressured shale gas wells in Yongchuan, Luzhou, and Dazu areas as research subjects. Through comprehensive methods such as log analysis, fluid inclusion analysis, and numerical simulation, the dominant mechanisms of strong overpressure formation were determined, and the pressure evolution from early burial to late strong uplift was characterized. Additionally, the impact of varying degrees of overpressure on reservoir pore characteristics was studied using techniques such as scanning electron microscopy, gas adsorption-mercury intrusion, and helium porosity testing. The research findings indicate that hydrocarbon generation expansion is the primary mechanism for strong overpressure formation. The pressure evolution in the early burial phase is controlled by the processes of kerogen oil generation and residual oil cracking into gas. The reservoir experienced three stages: normal pressure (Ordovician to Early Triassic), overpressure (Early Triassic to Early Jurassic), and strong overpressure (Early Jurassic to Late Cretaceous), with pressure coefficients of approximately 1.08, 1.56, and 2.09, respectively. During the late strong uplift phase, the adjustment of early overpressure occurred due to temperature decrease and gas escape, leading to a decrease in formation pressure from 140.55 MPa to 81.63 MPa, while still maintaining a state of strong overpressure. Different degrees of strong overpressure exert a significant control on the physical properties of shale reservoirs and the composition of organic matter pores. Variations exist in the organic matter pore morphology, structure, and connectivity within the deep Wufeng-Longmaxi shale. Higher overpressure favors the preservation of organic large pores and reservoir porosity. Under conditions of strong overpressure development, deep siliceous shales and organically rich clay shales exhibit favorable reservoir properties. By determining the dominant mechanisms of strong overpressure in the Wufeng-Longmaxi Formation and studying pore characteristics, this research not only deepens the understanding of the geological features of deep shale gas reservoirs but also provides a new perspective for understanding the overpressure mechanisms and reservoir properties of deep shale gas reservoirs. Moreover, it is of significant importance for guiding the exploration and development of deep Longmaxi shale and provides valuable references for further research in related fields.