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The Carboniferous Beizhan iron deposit is the largest submarine volcanic‐hosted iron deposit in the Awulale Iron Metallogenic Belt of the Western Tianshan. The magnetite‐dominated orebodies occur as lensoid, veined, and stratiform shape in the Dahalajunshan Formation which was intruded by basic‐acid intrusions. Skarn and carbonatization alteration are well developed around the orebody. The genesis of iron mineralization in Beizhan remains controversial. The calculated δ18O values of magnetite using the fractionation factor correspond to (or higher than) the range of common magmatic waters, as well as the δ18O values of alteration minerals (4.0–7.6‰) and intrusions (3.1–8.3‰), indicating magnetite and alteration minerals precipitation from magmatic hydrothermal fluids. The δ34S values of sulphides (pyrite and pyrrhotite) range from 1.0‰ to 6.4‰, supporting a magmatic hydrothermal origin for sulphur. Meanwhile, the Pb isotope compositions of iron ores overlap that of altered rock and intrusions, and the 187Os/188Os ratio of iron ores range from 1.5835 to 2.8452, in accordance with that of intermediate‐acid intrusions (e.g., K‐feldspar granite porphyry and syenodiorite), suggestive of magmatic hydrothermal fluids involved in the mineralization process. Furthermore, the magnetite from the ores shows higher MgO and MnO contents and lower content of TiO2. Pyrite samples from the ores show >570 ppm Co and Co/Ni ratios between 2.53 and 4.23. These features strongly point to a magmatic hydrothermal origin. Combined with previous studies, we propose that the submarine volcanic‐hosted Beizhan iron deposit is analogous to a skarn origin, driven by late‐stage hydrothermal fluids which originated from intermediate‐acid intrusions in the immediate vicinity.