The southeastern Yunnan region in the southwestern Nanpanjiang Basin is one of the most important manganese enrichment zones in China. Manganese mineralization is mainly confined to marine mud–sand–carbonate interbeds of the Middle Triassic Ladinian Falang Formation (T₂f), which contains several medium to large deposits such as Dounan, Baixian, and Yanzijiao. However, the geological processes that control manganese mineralization in this region remain insufficiently understood. Understanding the tectonic evolution of the basin is therefore essential to unravel the mechanisms of Middle Triassic metallogenesis. This study investigates how rift-related tectonic activity influences manganese ore formation. This study integrates global gravity and magnetic field models (WGM2012, EMAG2v3), audio-frequency magnetotelluric (AMT) profiles, and regional geological data to investigate ore-controlling structures. A distinct gravity low–magnetic high belt is delineated along the basin axis, indicating lithospheric thinning and enhanced mantle-derived heat flow. Structural interpretation reveals a rift system with a checkerboard pattern formed by intersecting NE-trending major faults and NW-trending secondary faults. Four hydrothermal plume centers are identified at these fault intersections. AMT profiles show that manganese ore bodies correspond to stable low-resistivity zones, suggesting fluid-rich, hydrothermally altered horizons. These findings demonstrate a strong spatial coupling between hydrothermal activity and mineralization. This study provides the first identification of the internal rift architecture within the Nanpanjiang Basin. The basin-scale rift–graben system exerts first-order control on sedimentation and manganese metallogenesis, supporting a trinity model of tectonic control, hydrothermal fluid transport, and sedimentary enrichment. These insights not only improve our understanding of rift-related manganese formation in southeastern Yunnan but also offer a methodological framework applicable to similar rift basins worldwide.