The Jiudingshan porphyry-skarn Cu-Mo deposit, located in the Sanjiang-Tethys metallogenic domain, is related to the left trending strike-slip fault of Jinshajiang-Ailaoshan tectonic belt. Field observations have identified the metal zonation in Jiudingshan, including the Mo-Cu mineralization in the inner porphyry system, Cu-Mo mineralization in the skarn system from the intrusion-carbonate contact zone, and the weakly Pb-Zn mineralization in the distal wall rocks. Trace element analyses on zircons from ore-bearing monzogranitic porphyry and porphyritic-like granite have yielded an average Ce4+/Ce3+ ratios of 218.0 and 218.6, respectively, which demonstrates an oxidative condition. Hydrothermal garnets from skarn system are well zoned and exhibit a large variation in Al and Fe contents. The dark cores of garnet are belong to andradite and enriched in LREEs, Mo and W, whereas the bright rims share an increase in Al and are enriched in Eu, U and Cu. Further Cu-Ag-Pb-Zn-Mo-W-Bi-Sn-As-Sb-Ti analyses on mineralized intrusions and orebodies have indicated a similar zonation observed in the field. The metals, like Cu, Ag and W, are commonly enriched in the same pattern while Mo shares no relationship with Cu. It can be concluded that an sulfur-unsaturated magma was more easily enriched and brought the Cu and Mo under high oxygen fugacity condition. The transition of Fe-rich to Al-enriched endmember in garnet from skarn system has suggested a fluid boiling process under a less oxidative condition. This process would inhibit the transportation of Mo complexes into skarn system but has the negligible impact on the solution of Cu, which finally led to the high Mo/Cu orebodies in porphyry system and high Cu/Mo orebodies in skarn system.