Objectives: Baogutu porphyry copper deposit is the first reduced porphyry copper deposit identified in central Asian metallogenic region, which shows different mineralogy characristics compared to oxidized porphyry copper deposit. Different metallic mineral assemblages are discovered in potassic alteration and phyllic alteration. With pyrrhotine, potassic alteration is characterized by chalcopyrite+molybedenite+pyrite+pyrrhotine+ilmentite+sphalerite±arsenopyrite assemblage. phyllic alteration is characterized by molybedenite+chalcopyrite+pyrite+arsenopyrite+sphalerite±Te—Bi minerals assemblage. pyrrhotine and arsenopyrite are resulted from different effects and show varied geological genetics. Methods: EPMA is employed to distinguish the chemical difference in sulfides. TerraSpec Halo is employed to identify minerals in advanced argillization. SEM is employed to identify the structural difference among sulfides in difference alteration stages. Results: Pyrite in different alteration stages shows difference in morphylogy. The chemical composition of pyrrhotine and arsenopyrite predicts its formation temperature (potassic alteration: 267~600℃; phyllic alteration: 209~325℃) and sulfur fugacity (potassic alteration: -1.5~-9.5; phyllic alteration: -15.8~-9.7). Kaolinite, illite and Magnetite are founded in advanced argillization stage. Conclusions: Combine the early research, we thought that there have different mineralization and sulfide assemblages in 1B potassic alteration stage and 1C sericite alteration stage. Pyrrhotine is precipatited in early reduced fluid. Arsenopyrite is resulted from the downturn of fS2 and temperature. 1B potassic alteration stage and 1C sericite alteration stage has experienced different chemical processes.