Various styles of ore deposits may form from a single magmatic-hydrothermal system. Identification of a possible genetic link between different ore types in a region is not only of critical importance for a better understanding of the magmatic-hydrothermal processes, but can also help in successful mineral exploration. Both iron oxide-apatite (IOA) and iron skarn deposits are closely associated with intrusive rocks of intermediate to felsic in composition, but whether these two ore types can form from the same magmatic intrusion remains poorly understood. In this study, we present a comparative study between a newly identified subsurface IOA ore body located at the apex of a diorite porphyry and the iron skarn ore bodies located immediately above it in the Jinniu volcanic basin of the Daye district, Middle-Lower Yangtze River metallogenetic belt (MLYRMB), eastern China in order to highlight a genetic link between these two styles of mineralization. The IOA ores are dominated by Ti-rich magnetite with variable amounts of fluorapatite, diopside, and actinolite. This mineralogical assemblage is distinctly different from the iron skarn ores, which consist mainly of Ti-depleted magnetite and subordinate pre-ore garnet and diopside, and post-ore quartz, chlorite, calcite, and pyrite. In addition, magnetite from the IOA ores is characterized by well-developed ilmenite lamellae and has high concentrations of Ni, V, Co, and Ga, consistent with high temperature crystallization, whereas magnetite grains from the iron skarn ores usually exhibit oscillatory growth zones and contain much lower Ni, V, Co, and Ga, indicating their formation under relatively low temperatures. Titanite and fluorapatite from the IOA ores have U-Pb ages of 132.5 ± 2.4 Ma to 128.4 ± 3.0 Ma, which match a titanite U-Pb age for the associated iron skarn ores (132.3 ± 2.0 Ma), and are consistent with zircon U-Pb ages for the ore-hosting diorite porphyry (130.4 ± 0.7 Ma to 130.3 ± 0.5 Ma). This age consistency supports a possible genetic link among the diorite porphyry, IOA ores, and iron skarn ores. We propose that the IOA and skarn ores are the products of two consecutive mineralization stages of the same magmatic-hydrothermal system, involving a high-temperature, hypersaline fluid coexisting with the diorite porphyry magma during emplacement and a subsequent low temperature, diluted hydrothermal fluid. Other IOA and iron skarn deposits of similar ages (130 Ma) are found in a series of volcanic basins in the MLYRMB, which forms one of the world’s largest IOA metallogenic belts. The close association of the two ore styles identified at Daye provides a useful exploration guide for IOA and iron skarn deposits both on a local and regional scale.