The Aqishan-Yamansu metallogenic belt (AYMB) in East Tianshan hosts abundant submarine volcanic-hosted iron deposits. Although there is agreement with the magmatic source of the ore-forming materials and the role of hydrothermal replacement in iron ore formation, the mineralization processes of these iron deposits remain uncertain. Three ore types are identified on the basis of the geological occurrences of minerals and the sequence of mineral in ores. The type I ores are characterized by magnetite, diopside, amphibole with a few pyrite, and chalcopyrite. The type II ores are mainly composed of magnetite, garnet, chlorite with a few pyrite, while the type III ores are mainly composed of magnetite, quartz, calcite with a few pyrite. In order to constrain the mineralization processes of these ore types, we performed iron isotopes and trace element compositions of magnetite from three typical iron deposits (Yamansu, Duotoushan and Luotuofeng). Trace element and Fe isotope investigations of the three ore types reveal two major groups. The group I consists of analyses of the type I and II ores, with both showing a narrow range of positive δ⁵⁶Fe values (+0.08‰ to +0.22‰ for type I ores and +0.15‰ to +0.22‰ for type II ores) and plotting in the range of the ortho-magmatic field. In contrast, the group 2 is composed merely of the type III ores, showing a wider range of negative δ⁵⁶Fe values (-0.49‰ to -0.01‰), which is similar to the features of Fe-skarn magnetite. As shown in the binary diagrams of magnetite trace elements and a fractionation of the Fe isotopes, different ore types were likely produced during gradually changing ore-forming stages from magmatic to hydrothermal. Collectively, the submarine volcanic-hosted iron deposits in the East Tianshan are likely the results of a continuous magmatic-hydrothermal mineralization process.