The Mamupu copper polymetallic deposit is characterized by multistage magnetite, but the genesis and fluid evolution process of this deposit are still obscure. Three types of magnetite were identified in Mamupu based on comprehensive textural observations and paragenesis. Mag1 occurs as subhedral to euhedral crystals, and smooth Mag1a and porous Mag1b can be distinguished under Backscattered Electron (BSE). Mag2 is characterized by 120° triple junction textures and has been replaced by hematite. Mag3 is commonly replaced by hydrothermal fluids and exhibits well-developed oscillatory zoning and core (Mag3a)-rim (Mag3b) textures. The geochemistry of Mamupu magnetite suggests that they are of hydrothermal origin. Mag1 has undergone extensive fluid-rock interactions, whereas the sharp contacts with Mag1a and Mag1b and the microporosity of Mag1b imply that the Mag1b was generated by the coupled dissolution reprecipitation of the Mag1a grains. This process may be triggered by low-temperature and high-salinity fluid produced by intensive water-rock interaction between ore-bearing magmatic-hydrothermal fluid and carbonate surrounding rock of the Jiaoga Formation. The 120° triple junction textures of Mag2 indicate that it was formed during a fluid-assisted recrystallization process, and Mag2 replaced by hematite represents the increase in oxygen fugacity. From Mag3a to Mag3b, the contents of V and Mn increased while the contents of chalcophile elements decreased, suggesting a decrease of oxygen fugacity and the precipitation of sulfide, which represents the beginning of the sulfide stage. Moreover, petrography and geochemistry data of magnetite represented that the breccia ore of Mamupu belongs to skarn mineralization. The geochemical characteristics of magnetite show that Cu-Au and W-Mo in Mamupu precipitated in different stages, representing the transformation from a relatively oxidized environment in the early stage to a relatively reduced environment in the late stage. These results reveal that trace elements in magnetite can be utilized to define the genesis and evolution of the skarn deposit. In addition, it can also restrict the precipitation mechanism of ore-forming elements in the deposits. However, detailed textural observations should be carried out before experimental research.