There are a wide range of magmatism and mineralization in the Yunkai area of South China during the Late Yanshanian Period, including the newly discovered Michang, Youmapo, Sanchachong and Songwang porphyry-skarn W-Mo deposits. In this study, we obtained zircon U-Pb ages of the ore-bearing biotite granites and their mafic enclaves from 88±1 to 110±1 Ma. Zircons from the granites show Hf isotopic compositions with negative ?Hf(t) values of -5.9 to -0.6 and calculated Hf model ages (TDM2) of 1.5–1.2 Ga; indicating that the Middle Proterozoic crustal materials may have provided an important source for the magmatic rocks in this district during the Late Yanshanian Period, whereas zircons from the mafic enclaves show positive ?Hf(t) values of 1.3 to 10.1 with younger Hf model ages (TDM2) of 0.5–1.1 Ga, suggesting a mantle component may have involved in the granitic magma generation. Sulfur isotope study of the sulfide minerals from the W-Mo deposits show a narrow δ34S distribution with most data ranging from -4.2‰ to 5.2‰. In addition, this study reports the first Fe isotopic compositions of pyrite in the W-Mo deposits, which show a uniform distribution range with the values near zero (δ56Fe=0.16‰–0.58‰, average 0.35‰; δ57Fe=0.02‰–0.54‰, average 0.48‰). These data indicate that the ore-forming materials may come from the deep-sourced granitic magma, and the mineralizations show a close relationship with the granitic magmatism during the Late Yanshanian Period. Combining with previous results, we suggest that there is a widespread porphyry-skarn W-Mo mineralization in the Yunkai area during the Late Cretaceous (80–110 Ma), which has a close relationship with the Late Yanshanian magmatism that may have formed during the rollback of the subducted Pacific Plate.