During the Middle Permian, Earth experienced a period of profound environmental changes, including the final stages of the Late Paleozoic Ice Age (LPIA), global seawater regression, the Guadalupian mass extinction event, and the eruption of the Emeishan Large Igneous Province (ELIP) in South China. These events collectively induced significant shifts in both the environment and biosphere, yielding several geochemical anomalies, including deposition of manganese (Mn) deposits. The link between Middle Permian Mn deposits and the prevailing environmental conditions, however, remains unclear. Here, four sections spanning the Middle Permian Maokou Formation to the Late Permian Longtan Formation in the Zunyi area of northern Guizhou, South China are investigated. Through sedimentological and geochemical analyses, this work aims to elucidate the evolution of sedimentary environments over the Middle to Late Permian. During this period, a transition from a shallow-water carbonate platform in the 1st Member of the Maokou Formation to a deeper, siliceous deposit in its 2nd Member was recorded. This shift results in a pronounced paleogeographic differentiation in the 3rd Member, juxtaposing the shallow-water carbonate platform against a deeper Mn-enriched basin. A number of geochemical proxies indicate a strong hydrothermal signal in the Mn deposits. Combined with positive Eu anomalies and low Sr isotopes, the data underscore the profound influence of hydrothermal input linked with early subaqueous eruptions from the ELIP on the nearby marine environment. A detailed examination of carbon isotope profiles from the Maokou Formation indicates that volcanic influences, shifts in marine ecosystems, and changes in primary production caused the fluctuations of δ13Ccarb and δ13Corg. Moreover, the formation of Mn carbonate in deeper waters effectively sequestered organic C. Collectively, our new data demonstrate that the essential conditions for the development of the carbonate-hosted Mn deposits include drowning of the carbonate platform through an increase in sea level, the availability of a sufficient Mn source, and the presence of a redox-stratified water column.