Economically important niobium (Nb), zirconium (Zr), gallium (Ga), and rare earth element deposits (Nb-Zr-Ga-REE polymetallic deposits) are widespread in the Emeishan large igneous province (ELIP), Southwest China. These deposits are hosted in the lower part of the Xuanwei Formation, which consists mainly of lacustrine sedimentary rocks overlain directly on ELIP basalts. While the close temporospatial correlation between these deposits and ELIP basalts has been recognized for a long time, their causal link is poorly understood. We analyzed major and trace elements, Hg concentrations, and Hg isotopic compositions of the lower part of the Xuanwei Formation. At three sites, the samples studied show enrichment in Nb (34.2−500 ppm), Zr (229−4220 ppm), Ga (33.6−138 ppm), and REEs and Y (REY; 123−2670 ppm). Multiple lines of evidence based on major and trace element analysis (e.g., Al₂O₃/TiO₂, Eu/Eu*, Nb/Yb, and REE distribution patterns) support that ELIP basalts are dominant source materials for the lower part of the Xuanwei Formation. High Hg concentrations (up to 335 ppb) and slightly negative to near-zero Δ¹⁹⁹Hg values (−0.19‰ to 0.11‰) were observed in the samples studied, which suggests that ELIP-derived Hg entered the lower part of the Xuanwei Formation via atmospheric deposition and weathering of ELIP basalts. This study highlights the crucial role of the ELIP eruption in the metallogeny of the Nb-Zr-Ga-REY polymetallic layers in the lower part of the Xuanwei Formation and can benefit our understanding of the genesis of supergene polymetallic deposits in large igneous province regions.