Iron oxide–apatite (IOA) deposits are important for the global supply of iron resources. Currently, there is considerable debate regarding the evolution of their mineralization mechanisms. The Heshangqiao iron deposit is a significant IOA deposit situated within the Ningwu ore district of the Middle–Lower Yangtze River Metallogenic Belt in China. This deposit exhibits distinct characteristics of multi-stage mineralization, forming disseminated ores, brecciated ores, and vein-type ores, from early to late stages. This study undertook a systematic elemental analysis of the magnetite and hematite from three mineralization stages of the Heshangqiao deposit. In the three mineralization stages of the Heshangqiao deposit, the elemental genesis indicators of ore genesis suggest that the hematite and magnetite both have magmatic hydrothermal genesis, characterized by high Ti and low Mg/Al and relatively high Ti and low Ni/Cr, respectively. The Cr and Sn contents of magnetite and hematite exhibit similar variation from the first to third mineralization stage, with an increase followed by a subsequent decrease. Meanwhile, the contents of V, Co, Ni, and Mn in magnetite and hematite exhibited an opposite trend, declining from the first to the second stage but eventually increasing from the second to the third stage. These changes in the genesis indicator also suggest that the multiple mineralization stages of the Heshangqiao deposit are independent of one another. The replacement of magnetite by hematite in each mineralization stage is not caused by the superposition of subsequent fluids, but rather by the residual fluid. It is noted that in the replacement the elements Cr, Co, and Ga were minimally migrated. These elements remained relatively stable and can be considered new potential discriminant indicators for the genesis of iron oxides.