The Indosinian granitoids, widely distributed in the northern margin of the West Qinling, are closely associated with the porphyry and skanz deposits spatio-temporally. The Wenquan large porphyry deposit, located in the Tianshui region, is characterized by low-grade molybdenum mineralization developed within and around porphyries and related to pervasive hydrothermal alteration zones. Pyrite, a ubiquitous mineral and a major constituent of porphyry stockwork veins at the Wenquan deposit. Study on chemical composition of pyrite could provide more constraints on fluid evolution and metal precipitation of magmatic-hydrothermal mineralization. 42 samples recording the sequence of vein formation independently were collected in numerous observation points throughout the deposit, based on intersection and overprinting relationships between different veins ( veinlets), intrusive contacts, and alteration types ( halos), four quartz stockwork veins are distinguished, as quartz-k-spar-biotite vein ( A-veinlet), quartz-chalcopyrite vein, quartz-molybdenite vein ( B vein) and quartz-sericite-pyrite vein ( D vein). The concentrations of Cu, Mo and Au of 101 pyrite grains in a suite of samples of four types quartz stockwork veins at Wenquan were determined by electron microprobe analysis ( EMPA), indicating that, A-veinlets, the earliest vein type recognized in magmatic-hydrothermal mineralization, are associated with biotite stable alteration, and represent the channel-ways for fluid causing alteration of former mafic minerals to biotite. Low concentrations of Cu, Mo and Au are detected in pyrites consistent to the fact that few sulfides precipitated during this stage. Quartz-chalcopyrite veins are closely related with potassic alteration with alteration of plagioclase to K-feldspar, and high Cu concentration of pyrite indicates the main stage of Cu mineralization. B veins, with higher Mo concentration of pyrite, as well as closely related to high grade Mo orebodies spatially, represent the main Mo mineralization stage. D veins, cutting and overprinting earlier quartz veins and cut by cracks filled with kaolinite and clays, as the last event of magmatic-hydrothermal mineralization, are filled mainly with pyrite and minor chalcopyrite and quartz, and closely associated with seritic alteration, which represent the Au and later Cu deposition stage.