The Huangshaping polymetallic deposit, located in southern Hunan Province in China, hosts abundant W–Mo–Pb–Zn mineralization that is associated with a large-scale skarn system at the contact zone between late Mesozoic granitoids and Carboniferous carbonates. To better understand the processes of polymetallic mineralization in the Huangshaping deposit, trace element concentrations of magnetites from different skarn stages were obtained by in situ laser ablation–inductively coupled plasma–mass spectrometry (LA–ICP–MS). The results show that two groups of magnetites were distinguished based on their trace element signatures. Group-1 magnetites, found in medium-grained garnet and calcite, have relatively low concentrations of Na, K, Ca, Si, Ge, Sn, and W, and relatively high concentrations of Mg, Al, Ti, V, Zn, Ni, and Co. The opposite is true for the Group-2 magnetites, which occur in coarse-grained garnet, tremolite, and bulk iron ore. These findings suggest that two compositional endmembers of hydrothermal fluids may be responsible for mineralization in the Huangshaping deposit. Group-2 magnetites likely precipitated from evolved magmatic hydrothermal fluids from which other minerals, such as garnet and tremolite, precipitated during the early skarn stages. The high Na, K, Ca, and Si contents of these hydrothermal fluids can be attributed to dissolution of the host rocks, which include limestone, sandstone, and evaporite horizons. On the other hand, the Group-1 magnetites precipitated from hydrothermal fluids with low Na, K, Ca, and Si contents. These low-salinity fluids may have been subjected to large-scale circulation, extracting Mg, Al, and Zn from the underlying Zn-rich metamorphic basement and the Mg- and Al-rich strata in this region. The high Ti, V, Ni, and Zn concentrations of Group-1 magnetites also suggest that these hydrothermal fluids had lower oxygen fugacity than the fluids from which the Group-2 magnetites precipitated. The results of this study demonstrate that the trace element concentrations of magnetites can be used to infer the composition and physicochemical conditions of the hydrothermal fluids from which they precipitated. In the case of the Huangshaping polymetallic deposit, this indicates that the hydrothermal fluids responsible for the W–Mo–Pb–Zn mineralization were derived from mixed sources.