The Zijinshan Cu-Au deposit, located in Fujian Province, is the largest high-sulfidation epithermal (HSE) deposit in Southeastern China and is usually regarded as a major part of the porphyry Cu system in the Zijinshan ore field. Molybdenite samples collected from the Cu mineralization zone yield a first weighted mean Re-Os age of 111.31 ± 0.70 Ma, which is explained as the time of dickite-alunite alteration. Combining the newly reported muscovite 40Ar-39Ar and zircon U-Pb ages (~113 Ma), the mineralization of Zijinshan is likely to initiate before ca. 110 Ma. This result is obviously older than the Re-Os age of the adjacent Luoboling porphyry Cu-Mo deposit (~105 Ma).Pyrite, chalcopyrite, bornite, digenite, and covellite collected from the deep potassic, middle phyllic and upper epithermal zones are used to conduct LA-ICP-MS trace element analysis. The spatial zonings of mineralization and alteration and the regular variations of trace elements in sulfides at vertical direction imply a potentially complete transition from porphyry to epithermal mineralization and the deep origin of ore-forming fluids. Mineralogical and trace element characteristics indicate that the chalcopyrite formed in both stages, whereas bornite is the product of epithermal mineralization, rather than a porphyry stage residue. The majority of digenite and covellite has hypogene genesis. Pyrite and digenite in the epithermal zone are major carriers of primary Au. Au in pyrite is Te-Bi related and exists as solid solutions or different-sized telluride and Bi-sulfosalt inclusions. Compared to As, Te and Bi played more important roles to scavenge Au and Ag and achieve the primary Au enrichment. Differently, Au in digenite is independently locked in digenite lattice. Bornite and digenite are good carriers of primary Ag, which mainly exists as solid solutions. The high sulfidation state stage is the major period for concentrations of primary Au and Ag. The upward increase of Au in primary sulfides of HSE Cu zone implies that the distribution pattern of upper Au enrichment and lower Cu enrichment is not only caused by supergene process, but is also controlled by hypogene trend.Based on the mineralization and alteration zonings, the spatial variation of trace elements and the presented Re-Os age, the ore-forming fluids of the Zijinshan Cu-Au deposit most likely originate from deep region, rather than from the adjacent Luoboling porphyry deposit. The Zijinshan and the Luoboling deposits should belong to two independent hydrothermal systems.