Multiple metallogenic types (skarn-type and vein-type) related to hypabyssal granites are found at the Huangshaping polymetallic deposit in the Nanling Range, South China. To constrain the crystallization and mineralization processes of skarn formation, three generations of magnetite and pyrrhotite from the hydrous silicate stage, oxide stage, early quartz–sulfide stage, and late quartz–sulfide stage were distinguished. The geochemical compositions of magnetite and pyrrhotite were obtained by electron probe microanalyzer (EPMA) and in-situ ablation-inductively coupled plasma-mass spectrometry (LA？ICP？MS). The results show that there may be silicate inclusions in magnetite and interaction of wall rock occurred in the mineralization process. The geochemical trends recorded in pyrrhotite show the influence of limestone during the crystallization of pyrrhotite. The re-equilibration temperatures of Po I, Po II, and Po III are 420.46, 380.45, and 341.81 °C, respectively, which suggests a continuous evolution following the high-temperature W–Sn mineralized system. The content change of Ni and V reflects a gradual decrease of oxygen fugacity from Mag I to Mag III, while the sulfur fugacity calculated from pyrrhotite gradually decreases. This continuous skarn mineralization evolution process helps us to better understand the change of metallogenic environment in the retrograde stage of the Huangshaping deposit.