During the Rhuddanian–Aeronian interglacial period, global geological events such as glacial melting, synsedimentary volcanic activity, biological resurgence, and large-scale marine transgressions caused frequent fluctuations in paleoproductivity, climate changes, and sea level variations. These paleoenvironmental transitions directly influenced the development characteristics of shale lithofacies. This study investigates the Longmaxi Formation shale in the Changning area in the Southern Sichuan basin, focusing on 28 core samples from Well N1. Using scanning electron microscopy, QEMSCAN, TOC, XRD, and major and trace element analyses, we reconstructed the paleoenvironmental transitions of this period and explored their control over shale lithofacies types and mineral compositions. Four shale lithofacies were identified: carbonate rich lithofacies (CRF), biogenic quartz-rich lithofacies (BQRF), detrital clay-rich lithofacies (CRDF), and detrital quartz-rich lithofacies (DQRF). During the Rhuddanian period, rising global temperatures caused glacial melting and rapid marine transgressions. The low oxygen levels in bottom waters, combined with upwelling and abundant volcanic material, led to high paleoproductivity. This period primarily developed BQRF and CRF. Rich nutrients and abundant siliceous organisms, along with anoxic to anaerobic conditions, provided the material basis and preservation conditions for high biogenic quartz and organic matter content. High paleoproductivity and anoxic conditions also facilitated the precipitation of synsedimentary calcite and supplied Mg2+ and SO42− for the formation of iron-poor dolomite via sulfate reduction. From the Late Rhuddanian to the Mid-Aeronian, the Guangxi orogeny caused sea levels to fall, increasing water oxidation and reducing upwelling and volcanic activity, which lowered paleoproductivity. Rapid sedimentation rates, stepwise global temperature increases, and the intermittent intensification of weathering affected terrigenous clastic input, resulting in the alternating deposition of CRF, CRDF, and DQRF. Two favorable shale gas reservoirs were identified from the Rhuddanian–Aeronian period: Type I (BQRF) in the L1–L3 Layers, characterized by high TOC and brittleness, and Type II (DQRF) in the L4 Layer, with significant detrital quartz content. The Type I-favorable reservoir supports ongoing gas production, and the Type II-favorable reservoir offers potential as a future exploration target.