The strongly deformed Yuleken porphyry Cu deposit (YPCD) occurs in the Kalaxiangar porphyry Cu belt (KPCB), which occupies the central area of the Central Asian Orogenic Belt (CAOB) between the Sawu’er island arc and the Altay Terrane in northern Xinjiang. The YPCD is one of several typical subduction-related deposits in the KPCB, which has undergone syn-collisional and post-collisional metallogenic overprinting. The YPCD is characterized by three pyrite-forming stages, namely a hydrothermal stage A (Py I), a syn-ductile deformation stage B (Py II) characterized by Cu-Au enrichment, and a fracture-filling stage C (Py III). In this study, we conducted systematic petrographic and geochemical studies of pyrites and coexist biotite, which formed during different stages, in order to constrain the physicochemical conditions of the ore formation. Euhedral, fragmented Py I has low Pb and high Te and Se concentration and Ni contents are low with Co/Ni ratios mostly between 1 and 10 (average 9.00). Py I is further characterized by enrichments of Bi, As, Ni, Cu, Te and Se in the core relative to the rim domains. Anhedral round Py II has moderate Co and Ni contents with high Co/Ni ratios >10 (average 95.2), and average contents of 46.5 ppm Pb and 5.80 ppm Te. Py II is further characterized by decreasing Bi, Cu, Pb, Zn, Ag, Te, Mo, Sb and Au contents from the rim to the core domains. Annealed Py III has the lowest Co content of all pyrite types with Co/Ni ratios mostly