Manganese carbonate ore samples from Nanhua System deposits (Hunan- Guizhou region) were collected from mining tunnels and drill cores for analysis by SEM, TEM, and XPS. Analytical results indicate pervasive replacement of manganese oxide by manganese carbonate within the ore, with both minerals forming multilayered, micrometer- scale microfossils that make up the bulk of the ore layers. Based on microstructural observations, the discovery of microfossils within manganese layers and nodules, and previous experimental simulations of microbial metabolism, this study analyzes the mechanisms by which microbial physiology controlled manganese deposition. The findings confirm that biochemical processes were fundamental to large- scale manganese mineralization. The marine sedimentary manganese deposits of the Nanhua System occur within the lower member of the Datangpo Formation in the Hunan- Guizhou- Chongqing region. The manganese ore layers across all mining districts consist of crystalline aggregates of rhodochrosite hosted within microbial fossils. During the metallogenic period, cyanobacteria- dominated microbial mat ecosystems proliferated extensively in the bottom- water environments of the South China Ocean shelf. Within these mats, cyanobacteria interacted with aerobic heterotrophic bacteria (AHB) and sulfate- reducing bacteria (SRB) through mutualistic symbiosis, controlling manganese precipitation and the transformation of manganese oxides to carbonates. Suspended mineral particles were either adsorbed onto surface sites of living microorganisms or self- aggregated within the spaces of autolytic dead cells. Manganese fluxes in seawater influenced microbial mats to deposit industrial- grade rhodochrosite ore layers intercalated with black shales. This study reveals that the biological activities through which microbial mats promoted the precipitation and transformation of manganese minerals were essentially survival mechanisms: ① analogous to modern manganese nodules, heterotrophic bacteria actively precipitate manganese oxides through enzymatic reactions while passively reducing manganese oxides through the metabolic byproducts of organic matter degradation; ② cyanobacteria actively regulated EPS microenvironments to maintain weakly alkaline and weakly reducing conditions while enhancing Mn2+ concentrations through heterotroph regulation, thereby enabling continuous passive precipitation of manganese carbonate minerals; ③ manganese carbonates and oxides precipitate simultaneously outside microbial cells, meaning deposition capacity is not constrained by the rate or capacity of cellular manganese absorption, enabling the transformation of abundant manganese supplies into massive mineral deposits; ④ the microbial life cycle represents a “pulsed” deposition cycle of manganese carbonates and oxides, where generational growth causes manganese minerals to stack layer upon layer, forming characteristic micrometer- scale mineral structures. This work establishes a biochemical “exogenic mineralization model” for marine sedimentary manganese deposits of the Nanhua System, advancing the “Endogenous Origin and Exogenous Mineralization” metallogenic theory of manganese.