The Dahongshan large-scale iron (Fe)–copper (Cu) polymetallic deposit is in the Proterozoic metallogenic domain on the western margin of the Yangtze Block. It is a typical representative of Fe-Cu polymetallic composite mineralization in the Kangdian area. The deposit comprises a group of layered orebodies formed by volcanic exhalation sedimentation and metamorphism, and a group of vein-like orebodies formed by hydrothermal superposition. The large-scale mapping of altered lithofacies in the deposit has resolved issues of weak links and unclear mineralization and alteration zoning of hydrothermal superimposed deposits within the study area. The mineralization type, hydrothermal alteration type and intensity, mineral assemblage, and mineral structure of the vein-type Cu polymetallic deposits during the hydrothermal superposition period are meticulously analyzed and studied. Finally, the zoning relationships of vein orebodies (mineralization) are summarized. On the basis of the results of the study of the distribution pattern of this mineral body, a mineralization alteration zoning model of the hydrothermal superposition period is constructed. The results show that the alteration is primarily silicification, carbonation, and chloritization, and the mineralization is chalcopyrite, bornite, chalcocite, and pyrite. The Dibadu anticline and the cutting layer faults and fractures strictly control the hydrothermal alteration zoning. The mineralization alteration zoning from the core to the flank is divided into coarse vein zone (I) → stockwork zone (II) → veinlet zone (III). The corresponding mineral assemblages are quartz–calcite–chalcocite–bornite–(native copper) (I) → calcite–dolomite–quartz–bornite–chalcopyrite–chlorite (II) → dolomite–quartz–chalcopyrite–(pyrite) (III), where the stockwork zone has the most substantial mineralization. The mineral assemblages of each alteration zone, the characteristics of rare earth elements of typical samples, and the test results on the fluid inclusions confirm that pH and Eh primarily control the zoning mechanism. This study has significance for deepening the understanding of the composite metallogenic system, guiding deep and peripheral prospecting, and providing significant enlightenment for the study of this type of deposit.