The Tongling ore district is one of the most economically important ore areas in the Middle–Lower Yangtze River Metallogenic Belt, eastern China. It contains hundreds of polymetallic copper–gold deposits and occurrences. Those deposits are mainly clustered (from west to east) within the Tongguanshan, Shizishan, Xinqiao, Fenghuangshan, and Shatanjiao orefields. Until recently, the majority of these deposits were thought to be skarn- or porphyry–skarn-type deposits; however there have been recent discoveries of numerous vein-type Au, Ag, and Pb-Zn deposits that do not fall into either of these categories. This indicates that there is some uncertainty over this classification. Here, we present the results of several systematic geological studies of representative deposits in the Tongling ore district. From investigation of the ore-controlling structures, lithology of the host rock, mineral assemblages, and the characteristics of the mineralization and alteration within these deposits, three genetic types of deposits (skarn-, porphyry-, and vein-type deposits) have been identified. The spatial and temporal relationships between the orebodies and Yanshanian intrusions combined with the sources of the ore-forming fluids and metals, as well as the geodynamic setting of this ore district, indicate that all three deposit types are genetically related each other and constitute a magmatic–hydrothermal system. This study outlines a model that relates the polymetallic copper–gold porphyry-, skarn-, and vein-type deposits within the Tongling ore district. This model provides a theoretical basis to guide exploration for deep-seated and concealed porphyry-type Cu (–Mo, –Au) deposits as well as shallow vein-type Au, Ag, and Pb–Zn deposits in this area and elsewhere.