During the interglacial period of the Cryogenian glaciation, the extensive “Datangpo-type” manganese ores were deposited in the Nanhua Basin. However, there has been significant controversy over the precipitation mechanism of manganese for decades. Based on iron and nitrogen isotope data from the manganese ores of the Datangpo Formation in Chongqing (South China), combined with previous research, we propose that the manganese ores of the Datangpo Formation precipitated directly in an anoxic bottom-water environment in the form of rhodochrosite. The δ⁵⁶Fe values in the Bijiashan manganese ore (δ⁵⁶Fe = −0.19 ± 0.13 ‰) are close to those of modern marine hydrothermal iron, and there is a strong positive correlation between the δ⁵⁶Fe value and iron concentration (R² = 0.81), indicating that the precipitation of manganese ore could be mainly affected by hydrothermal input. After comprehensively comparing the δ⁵⁶Fe values of the whole rock and pyrite in the manganese ore of the Datangpo Formation, we believe that iron from hydrothermal sources directly and quantitatively combined with sulfides to form pyrite. Additionally, the bottom seawater of the basin was mainly anoxic. The nitrogen isotope composition indicates the presence of a stable nitrate reservoir in the ocean at that time, and manganese ore deposition may have been influenced by the input of high-salinity water from the open ocean. Due to the supply of NO₃^- from the open ocean to the graben basin, the δ¹⁵N in manganese ore is significantly higher than that in black shale. The input from the open ocean led to an increase in alkalinity in the bottom water of the basin, which favored the precipitation of rhodochrosite. Considering that the oxidation potential required for manganese oxidation precipitation is higher than that required for iron oxidation precipitation, it is most reasonable to conclude that under alkaline anoxic conditions in the bottom water layer, Mn²⁺ directly precipitated in the form of rhodochrosite.