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Deep-water ferromanganese (Fe-Mn) nodules cumulate trace elements from the underlying sediment pore-water and seawater during the concentric mineral layers' growth process over millions of years. They can record long-term tectonic movements and paleoceanographic changes. To systematically ascertain paleoceanographic evolution of the deep South China Sea (SCS) since the last 3.2 Ma, we comprehensively investigated microstructure, mineralogy, geochemical element concentrations as well as Sr, Nd and Pb isotopic compositions in the Fe-Mn nodules nearby the Dongsha Islands in the northern SCS. Results indicate that these deposits were formed in a continental marginal environment by a mixture of diagenetic and hydrogenetic processes. Overall, the studied nodules can be divided into three stages with different microstructures and chemical compositions, which indicate different formation environments. Stage la is the innermost and oldest layer with a porous mottled texture, and has the lowest Mn/Fe ratio, Cu, Ni and Zn, which implies comparatively high oxidization conditions. In contrast, the Mn mineralogy of Stage 2 shows conditions similar to those of buserite formed under less oxidative conditions. Between Stage la and 2, Stage 1b represents a mixture of Stage la and 2 and has in homogeneous growth structures. Based on the Nd and Sr isotopic composition of the detrital phases and Pb isotopes, three potential terrigenous source regions including South China, Luzon and Taiwan that discharge into the northern SCS from 3.2 Ma to 1.06 Ma. After 1.06 Ma, the terrigenous fraction in the Fe-Mn deposits on the northern slope of the SCS is a two end-members mixture of fluvial input from Taiwan Islands and eolian dusts from the Chinese loess. Our study indicates that SCS bottom water variation occurred at similar to 3.2 Ma, 2.1 Ma, and 1.06 Ma, respectively, which could be attributed to global cooling and the influence of Luzon arc-forearc uplift.