The genetic mechanism of the Lower Triassic Dongping carbonate-hosted Mn deposit in South China remains debated, particularly regarding depositional redox conditions and the role of organic matter in Mn carbonate formation. Here we present an integrated sedimentological and geochemical study based on new drill-core materials from the Lower Triassic Mn-bearing succession of the Shipao Formation in the Youjiang Basin. The ore bodies are mainly stratiform and locally exhibit stromatolitic fabrics. Mn-bearing minerals are dominated by kutnohorite, which commonly contains calcite or dolomite nuclei. The Mn-bearing interval is carbonate-dominated and characterized by persistently low TOC contents. Weak authigenic enrichment of redox-sensitive trace metals (Mo, U, and V) in Mn-bearing carbonates, indicates deposition under predominantly oxic to at most suboxic bottom-water conditions. Paleo-productivity proxies (biogenic Ba) indicate relatively high surface-water primary productivity during deposition of the Mn-bearing succession. Notably, the limited accumulation of organic matter despite high paleo-productivity suggests that bottom waters remained oxygenated. Moreover, the predominance of positive Ce anomalies (Ce/Ce*) in Mn carbonates indicated they experienced the Mn-oxide precipitation stage. The negative correlation between Mn contents and Mn carbonate δ13C values indicates a significant contribution of organic-derived DIC, likely mixed with seawater and/or carbonate-derived DIC, during Mn carbonate precipitation. These observations support a two-stage sedimentary–diagenetic model in which Mn oxides initially formed and accumulated in an oxic water column and were subsequently reduced during early diagenesis in anoxic pore waters, generating Mn2+- and HCO-3-rich fluids that promoted Mn carbonate precipitation. Petrographic observations further suggest that authigenic carbonate substrates, and possibly microbial influence inferred from stromatolitic fabrics, facilitated Mn carbonate nucleation and growth. This process-based model refines the organo-diagenetic transformation framework for the Dongping deposit and provides improved facies- and mechanism-oriented criteria for exploration of Mn carbonates within the Shipao Formation, with broader implications for carbonate-hosted Mn systems in South China.