The Makeng iron deposit in southwest Fujian is a significant iron polymetallic deposit containing various types of iron ore, including garnet magnetite, diopside magnetite, and quartz magnetite. The metallogenetic type of the deposit has been a subject of debate, particularly in relation to the genesis of magnetite and the source of iron. In situ microanalysis of trace elements in magnetite from different ores shows relatively low levels of V, Ti, Cu, and Zn, with higher concentrations of Ca and Si, indicating the characteristics of a skarn type deposit. The δ57Fe values of the magnetite range from −0.091‰ to 0.317‰. Combining these data, whole-rock iron isotope analyses, including Juzhou and Dayang granites, diabase, and the Lower Carboniferous Lindi Formation sandstone, suggest that Fe in the magnetite primarily originates from granitic pluton, with potential contributions from diabase and the Lower Carboniferous Lindi Formation sandstone. Combined with field work, these results indicate that Makeng iron deposit is a skarn-type magnetite deposit associated with Yanshanian granitic intrusions. Therefore, the initial ore-forming fluid is postulated to be a high-temperature magmatic hydrothermal fluid with high oxygen fugacity. This fluid infiltrates spaces such as interlayer fracture zones between the Upper Carboniferous Jingshe Formation–Middle Permian Qixia Formation carbonate rocks and the Lower Carboniferous Lindi Formation sandstone, resulting in diverse magnetite ores due to metasomatism. The mineralization process of the Makeng iron deposit is basically the same, as it is composed of typical skarn deposits. Magnetite was mainly formed during calcic skarn formation stage, and this process persisted until the initial phase of the retrograde alteration of skarns. In contrast, sulfide minerals, including molybdenite, sphalerite, and galena, precipitated during the quartz–sulfide stage.