The supergiant Shizhuyuan W–Sn–Bi–Mo deposit is hosted by the Qianlishan granite, a small, highly fractionated granitic pluton (~10 km2) with multiple phases of intrusions within the Early Yanshanian granitoid province of SE China. Strong alteration of skarn and greisen that formed in the contact zone between the first and second phases of granite intrusions and Devonian limestone is responsible for the polymetallic mineralizations. SHRIMP U–Pb zircon analysis indicates that the two early phases of the Qianlishan granite formed contemporaneously at 152 ± 2 Ma. Metasomatic minerals (garnet, fluorite and wolframite) separated from the skarn and greisen yield a Sm–Nd isochron age of 149 ± 2 Ma that is interpreted as the formation age of the Shizhuyuan deposit. Therefore, the mineralization of the supergiant Shizhuyuan polymetallic deposit formed contemporaneously with, or very shortly after, the intrusion of the small, highly fractionated Qianlishan granite.