The Jinkeng Sn-Cu polymetallic deposit in South China consists of two different types of orebodies: 1) NE-striking skarn- and vein-type Cu-Pb-Zn-Sn orebodies in volcanic rocks suffering subsequent ductile shear deformation, and 2) NW-striking quartz-cassiterite-sulfide veins filled in the faults at the porphyritic granodiorite outward from the fine-grained granite which does not exhibit deformation. The relationships among Sn-Cu polymetallic mineralization, regional magmatism, and deformation metamorphism are still controversial. To address it, the geochronological, whole-rock and mineral geochemical research along with the detailed field investigation were conducted in this study. Our zircon U-Pb dating results show that the volcanic rocks formed at 158–162 Ma, earlier than the porphyritic granodiorite which yields the emplacement age of 146–147 Ma. In-situ LA-ICP-MS U-Pb dating of cassiterite from the deformed skarn ores indicates the early-stage mineralization occurred at 146 ∼ 148 Ma, which is similar to the emplacement age of the porphyritic granodiorite, but earlier than the formation of quartz-cassiterite-sulfide veins and the fine-grained granite (141∼144 Ma). Further, the whole-rock and biotite geochemistry, and zircon Hf isotope compositions suggest that the porphyritic granodiorite exhibits a lower degree of magma differentiation, higher oxygen fugacity, higher Cl and lower F contents than the fine-grained granite. The porphyritic granodiorite might provide the most Cu-Pb-Zn budget accompanied by minor Sn for early-stage mineralization. Overall, our study suggests that the Jinkeng Sn-Cu polymetallic deposit formed in two scenarios where the early dominated Cu-Pb-Zn and minor Sn mineralization related to the emplacement of the porphyritic granodiorite is superimposed by the late vein-type Sn-dominated mineralization related to the emplacement of the fine-grained granite. The two isolated mineralizing events (∼147 Ma and ∼141 Ma, respectively) in Jinkeng were probably responded to the regional magmatic activities triggered by the tectonic transformation where two extensional tectonic events were separated by a short contractional event (147–144 Ma).