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The Great Xing'an Range in north‐eastern China hosts numerous super‐large Ag–Pb–Zn deposits and some Fe–Sn deposits. The Mesozoic Haobugao Fe–Zn polymetallic skarn deposit in the southern Great Xing'an Range is contemporaneous with the regional Ag–Pb–Zn mineralization. Numerous ore bodies are hosted in the Lower Permian carbonate strata or along the contact with the Early Cretaceous granite. According to the field and systematic petrography and mineralography research, the Haobugao mineralization phases are divided into 3 paragenetic stages: prograde stage, retrograde stage, and sulphide stage. Magnetite mainly occurred in the retrograde stage and replaced the anhydrous skarn minerals (e.g., garnet and diopside). Two types of magnetite (Mag1 and Mag2), including 6 subtypes, can be distinguished based on the scanning electron microscopy and back scattered electron images. Electron probe microanalysis and laser ablation inductively coupled plasma mass spectrometer analysis were used to determine major and trace elements in different types of magnetite. Mag1 has higher Ti and V concentrations than Mag2, indicating a relatively higher depositional temperature. Mag1 also contains relatively higher Mg and Mn concentrations, coupled with much lower Si and Al concentrations, which reflects a low fluid/rock ratio at the site of Mag1 deposition. Element variation features of Mag1 and Mag2 reveal that the Haobugao mineralization fluids gradually evolved from high‐temperature and low fluid/rock ratio fluids to relatively low‐temperature and high fluid/rock ratio fluids. However, electron probe microanalysis data of Mag2 display significantly higher Sn concentrations (up to 2.82 wt.%) than that in Mag1, which indicates that Sn can be incorporated into magnetite crystal lattice. We propose a possible substitution mechanism of Sn4+ + Mn2+ = 2Fe3+, supported by the strongly positive correlation between Sn4+ and Mn2+, whereby a substitution of Sn4+ for Fe3+ in octahedral sites of magnetite requires a compensatory substitution of Mn2+ for Fe3+ to maintain the charge balance. [ABSTRACT FROM AUTHOR]