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The Panjia polymetallic deposit, located in the northwestern region of Zhejiang Province, is a newly discovered medium‐ to large‐sized W–Mo–Cu ore deposit belonging to the northern part of the Qinzhou Bay–Hangzhou Bay metallogenic belt. Through investigation in the field and under the microscope, the hydrothermal activity of this deposit can be divided into four stages: pre‐ore stage, silicate oxidation stage, quartz sulfide stage, and post‐ore stage. The Datongkeng pluton, outcroping in Panjia deposit, is one S‐type intrusive rock and characterised by concentrations of SiO2, K2O and Na2O ranging from 67.03 to 71.09%, 3.03 to 4.89%, and 0.24 to 3.37%, respectively. The major elements display peraluminous, high‐K, calc‐alkaline features. Their A/CNK(A/CNK = n (Al2O3)/ [n (CaO) + n (Na2O) + n(K2O)]) ratios, δEu values, and δCe values vary from 0.93 to 1.98, 0.45 to 0.91, and 0.93 to 1.07, respectively. These rocks are enriched in light rare earth elements (all record values of (La/Yb)N <10, except for one) whereas are depleted in Sr, Ba, Nb, P, Eu, and Ti. The end‐member study of the Pb and S isotopes shows that the mantle material plays an important role in the ore‐forming. Zircon U–Pb dating indicates that the second part of the multiperiod magmatism (154–150 Ma) of Datongkeng pluton is the relevant crystallisation age, and the study of metallogenic stage manifests that the molybdenite is formed at the third stage of the mineralisation sequence considered as the main period of mineralisation, subsequent to the mineralogenetic epoch of scheelite. The petrogenesis is related to the materials in the crust and a small amount of materials in the mantle. While the low degree of mantle source and the Proterozoic basement contribute to the Mo, Cu ore‐forming materials. Finally, two types of metallogenic assemblage are formed, including the W‐Mo polymetallic deposit in the Datongkeng pluton and the W‐Cu‐Pb‐Zn‐Ag polymetallic deposit in the veins in the Lantian Formation. [ABSTRACT FROM AUTHOR]