The Jiama copper polymetallic deposit is a super large porphyry skarn deposit of great economic value and scientific research significance in the eastern part of the Gangdise metallogenic belt, which completely preserves important information on the formation and evolution of skarn deposits. Previous studies mostly focused on the horizontal zoning of skarn, but the vertical zoning of skarn minerals and its coupling relationship with metal mineralization is less understood. This paper focuses on the detailed mineralogical study of skarn ore body in the Jiama 3000 m scientific deep borehole, and systematically reveals the mineralogical spatial zoning characteristics of skarn ore body and its coupling relationship with metal mineralization. The results show that the skarn has clear zoning from shallow to deep, i.e. skarn hornfeld→diopside garnet skarn→wollastonite garnet skarn→garnet wollastonite skarn→diopside garnet skarn→garnet wollastonite skarn→Skarn marble→wollastonite garnet skarn→diopside garnet skarn→diopside garnet skarn→wollastonite garnet skarn→skarn marble→wollastonite garnet skarn→wollastonite garnet skarn→skarn marble→wollastonite garnet skarn→diopside garnet skarn→endoskarn (containing garnet granodiorite porphyry). The metal mineral assemblage changes from shallow to deep, molybdenite±chalcopyrite→bornite+chalcopyrite±chalcocite±wittichenite±(molybdenite) →molybdenite±chalcopyrite. The corresponding metallogenic elements are Mo±Cu±Au±Ag→Cu(Mo)±Au±Ag→Mo±Cu±Au±Ag. The research shows that the spatial location of intrusive and surrounding rocks, tectonic settings and the superposition of multi-stage hydrothermal fluids are important factors controlling the zoning of skarn minerals. At the same time, the mineralogical characteristics show that the enrichment of high-grade gold in skarn is closely related to copper sulfides such as bornite, and may also be related to the superposition of multi-stage fluids and the source area of gold-rich magma.