Pyrite geochemistry has been extensively used to reveal ore-forming processes in diverse ore deposits, but its application in skarn systems is not well understood. The Huangshaping deposit in the Nanling Range (South China) uniquely develops W–Sn–Pb–Zn and Cu–Pb–Zn skarn mineralization systems, and both two systems have formed multi-types of pyrite, which provides a good window to reveal the mineralization histories of different skarn systems using pyrite trace element geochemistry. In the Cu–Pb–Zn system, texturally homogeneous Py1 mainly occurs in calcite veins within the host rock, whereas texturally homogeneous Py2 in the calcite-sulfide stage mainly occurs in skarn orebodies. Py3 in the siderite-sulfide stage replaces Py2 and commonly develops abundant pores or fractures, resembling the “bird's eye” texture. In the W–Sn–Pb–Zn system, Py4 in calcite veins can be divided into the oscillatory-zoned Py4a and irregular Py4b under BSE, and Py4b commonly replaces Py4a as veins or overgrowth. Texturally homogeneous Py5 in the calcite-sulfide stage occurs in skarn orebodies and is replaced by Py6 with a “bird's eye” texture in the siderite-sulfide stage.In the Cu–Pb–Zn system, Py1 may have formed by fluid cooling during its ascent along the hydraulic fractures indicated by its enrichment of Co, Ni, As, Sb, and Tl, whereas Py2 is likely formed under higher temperature and pH conditions caused by intense fluid-rock interactions evidenced by its depletion of Co, Ni, As, Sb, and Tl as well as its enrichment of Zn and Ag. In the W–Sn–Pb–Zn system, Py4b has higher contents of Co, Ni, As, Sb, and Tl than Py4a and similar contents of Ag, Zn, and Mo with Py4a, suggesting that decreasing temperature may have controlled the formation of Py4b. Py5 is featured by the depletion of As, Sb, Tl, and Mo as well as the enrichment of Zn and Ag, indicating that Py5 is likely formed under higher temperature and pH conditions resulting from the intense fluid-rock interactions. Marcasite replaces pyrrhotite and then is replaced by pyrite may be an important precipitation mechanism for pyrite with a “bird's eye” texture (Py3 and Py6) in both two skarn systems at Huangshaping. This study demonstrates that fluid-rock interaction is an important mechanism for sulfide precipitation at Huangshaping, which shows that pyrite geochemistry has good potential to reveal mineralization histories in skarn systems.