South China hosts a large number of Middle Permian marine sedimentary Mn deposits (MSMDs) coeval to the eruption of the Emeishan Large Igneous Province (ELIP). The linkage between these MSMDs and ELIP eruption remains unclear. Here, we observed anomalously high Hg concentrations and Hg/TOC ratios, and a shift of Δ199Hg to near-zero at the base of the Middle Permian Zunyi MSMD. These results suggest ELIP eruption as a possible driving force for the deposition of the Zunyi MSMD. Principal component analysis (PCA) of trace element concentrations of the Zunyi MSMD samples revealed three clusters of trace elements. Cluster A elements (Cr, Zn, Mo, Sb, and Tl) are anomalously high at the basal of the Zunyi MSMD, confirming ELIP as a driver for the formation of this deposit. Cluster B elements (Ba, Rb, and Cu) are high in the entire deposit, supporting elevated oceanic productivity. A stepwise increase in Cluster C elements (Li, Ga, Sn, Zr, Nb, Hf, Ta, and W) concentrations in the Zunyi MSMD suggests enhanced terrestrial weathering. We infer that the ELIP eruption triggered an increased input of terrestrial nutrients to the ocean, causing increased oceanic productivity and rising dissolved O2 levels in the surface water of the middle Permian ocean in South China, favoring Mn deposition and MSMDs formation.