Most molybdenum (Mo) deposits are considered to be associated with magmatic systems; however, their genetic link is not clearly resolved when using, for example, bulk sulfur (S) and lead (Pb) isotopes of sulfides dominated by pyrite separates. Here, we present microtextures and in situ trace-element results of pyrite, in situ S isotopic compositions of molybdenite and pyrite, and Pb isotopes of pyrite and K-feldspar determined by laser ablation−inductively coupled plasma−mass spectrometry (LA-ICP-MS) and multicollector (MC) LA-ICP-MS. Combined with geochronologic data for both the magmatism and Mo mineralization, these in situ methods allowed the genetic link between Mo mineralization and magmatism to be unraveled at Shipingchuan, SE China. The Shipingchuan deposit is characterized by molybdenite-quartz veins hosted by faults or fractures around a biotite K-feldspar granite. Zircon LA-ICP-MS U-Pb and molybdenite Re-Os dating results confirm that the biotite K-feldspar granite and mineralization were coeval and formed during the end of the Early Cretaceous (ca. 105 Ma), whereas postmineralization monzogranite porphyry dikes formed at 93.7 Ma. Pyrite shows a close mutual relationship with molybdenite and is characterized by Co-Ni-As-Te-Cu-Pb-Ag-Bi−rich cores (PyI) revealed by LA-ICP-MS data. Co/Ni and calculated (Se/S)fluid ratios for both cores (PyI) and rims (PyII) indicate a magmatic-hydrothermal origin. The in situ S isotopic compositions (δ34S) of molybdenite are 2.1‰ to 6.8‰, which are identical to those of molybdenite separates. PyI has δ34S values of −6.9‰ to 0.8‰, whereas PyII exhibits slightly more negative values of −7.5‰ to −0.2‰. These analyses indicate reliable results for in situ S isotopes in molybdenite, which could be more appropriate to constrain the origin of sulfur in hydrothermal fluids than results from pyrite analysis. The in situ S isotopic compositions of sulfides confirm a magmatic source for sulfur. The in situ Pb isotopic compositions of pyrite are consistent with those of K-feldspar from the biotite K-feldspar granite, indicating a common source. The heterogeneous As/Ni, As/Sb, and As/Bi values, as well as the variations of δ34S values of both PyI and PyII, indicate progressive oxidization of the hydrothermal fluids. These results illustrate that the metal-rich fluids were released from the granite and migrated along faults and fractures around the granite in an extensional setting. The precipitation of molybdenite-quartz veins at Shipingchuan was triggered by changes in temperatures and redox conditions, which were caused by mixing of magmatic fluids and meteoric water. Results in this study provide an example of tracing the link between Mo mineralization and magmatism using in situ S isotopic compositions of molybdenite and Pb isotopes of pyrite and K-feldspar.