The Dahongshan Fe-Cu (-Au) deposit is a superlarge deposit in the Kangdian metallogenic belt, southwestern China, comprising approximately 458 Mt of Fe ores (40% Fe) and 1.35 Mt Cu. Two main types of Fe-Cu (-Au) mineralization are present in the Dahongshan deposit: (1) early submarine volcanic exhalation and sedimentary mineralization characterized by strata-bound fine-grained magnetite and banded Fe-Cu sulfide (pyrite and chalcopyrite) hosted in the Na-rich metavolcanic rocks; (2) late hydrothermal (-vein) type mineralization characterized by Fe-Cu sulfide veins in the hosted strata or massive coarse-grained magnetite orebodies controlled by faults. While previous studies have focused primarily on the early submarine volcanic and sedimentary mineralization of the deposit, data related to late hydrothermal mineralization is lacking. In order to establish the metallogenic age and ore-forming material source of the late hydrothermal (-vein) type mineralization, this paper reports the Re-Os dating of molybdenite from the late hydrothermal vein Fe-Cu orebody and H, O, S, and Pb isotopic compositions of the hydrothermal quartz-sulfide veins. The primary aim of this study was to establish the metallogenic age and ore-forming material source of the hydrothermal type orebody. Results show that the molybdenite separated from quartz-sulfide veins has a Re-Os isochron age of 831 ± 11 Ma, indicating that the Dahongshan Fe-Cu deposit experienced hydrothermal superimposed mineralization in Neoproterozoic. The molybdenite has a Re concentration of 99.7–382.4 ppm, indicating that the Re of the hydrothermal vein ores were primarily derived from the mantle. The δ34S values of sulfides from the hydrothermal ores are 2‰–8‰ showing multi-peak tower distribution, suggesting that S in the ore-forming period was primarily derived from magma and partially from calcareous sedimentary rock. Furthermore, the abundance of radioactive Pb increased significantly from ore-bearing strata to layered and hydrothermal vein ores, which may be related to the later hydrothermal transformation. The composition of H and O isotopes within the hydrothermal quartz indicates that the ore-forming fluid is a mixture of magmatic water and a small quantity of water. These results further indicate that the late hydrothermal orebodies were formed by the Neoproterozoic magmatic hydrothermal event, which might be related to the breakup of the Rodinia supercontinent. Mantle derived magmatic hydrothermal fluid extracted ore-forming materials from the metavolcanic rocks of Dahongshan Group and formed the hydrothermal (-vein) type Fe-Cu orebodies by filling and metasomatism.