Many manganese (Mn) carbonate deposits over geologic history are often closely associated with black shales. However, the mechanism(s) by which the Mn entered the sediments remains controversial because on one hand oxygenated waters are required for primary Mn(IV) oxide formation but on the other hand black shales generally form under reducing conditions. China hosts some of the world’s largest black shale-hosted Mn deposits, for example, the Carboniferous Ortokarnash and Malkantu Mn deposits in the Malkansu region, offering a good opportunity to revisit the genesis of black shale-hosted Mn carbonate deposits. Here, we present the first coupled, systematic paleoredox and hydrographic reconstruction of those deposits with the aim of elucidating the redox-state of the depositional basin at the time of their initial deposition. The Mn ore beds in this region are hosted within laminated, organic-rich mudstones (i.e., black shales) reflective of a relatively deep-water depositional environment. The Mn ores are comprised of the Mn(II) carbonate minerals (rhodochrosite and Ca-rhodochrosite), with minor alabandite, pyrite, and monazite. Multiple independent lines of evidence, including positive shale-normalized Ce anomalies (average 3.0), negative δ13CVPDB values (average −11.55 ‰), and negative δ98MoNIST+0.25 values (average −1.07 ‰), indicate that the Mn(II) carbonate ores were formed during diagenesis via the coupled oxidation of organic matter and reduction of Mn(IV) oxides originally deposited from an oxygenated water column. However, in apparent contradiction, highly reactive iron to total iron (FeHR/FeT; average 0.66) and pyrite iron to highly reactive iron (FePy/FeHR; average 0.71) ratios, combined with a high abundance of small framboidal pyrites (mean diameter ∼5 μm) with narrow size ranges (standard deviations <2 μm), suggest that the associated black shales were deposited in euxinic (H2S-bearing) bottom waters. Euxinia resulted from sluggish water mass circulation, with sedimentary Mo/TOC ratios indicating a relatively strong hydrologic restriction. During this stage, dissolved Mn(II) would have accumulated in euxinic waters but not become permanently fixed into sediments, as indicated by higher degrees of enrichment for Mo over U and lower Mo isotope values than coeval seawater recorded in the black shales. These reveal an active Mn(IV) oxide shuttle across a redox-stratified water column. Combined, the Mn ore intervals document sharp benthic oxygenation of euxinic bottom waters, a process that might be induced by the periodic incursions of oxic seawater associated with eustatic sea level rises. This model is supported by the Mo isotopic characteristics of the Mn carbonate ores, which indicate original Mn oxide precipitation from an overlying water with Mo isotopic composition close to coeval open seawater (minimum δ98MoNIST+0.25 of 1.9 ‰). In contrast to the generalized “bathtub ring” model envisaging that the black shale-hosted Mn deposits were formed at shallow basin margins, our results highlight that they were more likely formed by in-situ ventilation of anoxic (especially euxinic) deep waters of basin center settings. In this regard, we suggest that the ventilation model better explains the close association of Mn carbonate ores with black shales, and has profound implications for understanding the paleoredox framework of otherwise Mn-rich black shale successions.