Granite-related W-Sn ore systems are commonly associated with coeval Pb-Zn mineralization. It remains unclear whether these metals are derived from the same sources or not. Mercury (Hg) is a common minor component in such systems. Hg isotopes undergo unique mass-independent fractionation (expressed as Δ¹⁹⁹Hg values), which is mainly generated during Hg photochemical reactions on Earth’s surface and not affected by magmatic-hydrothermal processes, offering an excellent opportunity to trace metal sources in hydrothermal systems. We observed near-zero Δ¹⁹⁹Hg values in wolframite (−0.10‰ to 0.08‰, n=11), and in skarn- (−0.17‰ to 0.12‰, n=48) and greisen-type (−0.12‰ to 0.10‰, n=11) bulk tin-tungsten ore from eight major ore deposits in South China. These values are identical to those of coeval highly evolved granites (−0.13‰ to 0.12‰, n=49), supporting that Hg in W-Sn ores were sourced from granite. However, sulfides (e.g., pyrite, chalcopyrite, arsenopyrite, galena, and sphalerite) in these deposits exhibit negative to near-zero Δ199Hg values (−0.42‰ to 0.09‰, n=124), which indicates a contribution of Hg and by inference other metals from both Precambrian basement rocks (Δ¹⁹⁹Hg<0) and ore-related granites. The study demonstrates that multiple sources of metals were involved in the formation of the polymetallic W-Sn deposits, and further highlights that extraction of metals from basement rocks may be a critical control on the formation of economically important mineralization of base metal sulfides (e.g., Pb, Zn) in granite-related magmatic-hydrothermal systems.