Trace element compositions of magnetite of alkaline mafic–ultramafic rocks were not previously studied but are potentially useful to constrain their petrogenesis and related metallogenesis. In the Permian Emeishan large igneous province, subalkaline mafic–ultramafic intrusions are widely distributed, but sparse alkaline counterparts are recognized, including the Mouding intrusion. The alkaline intrusions are mainly composed of clinopyroxenite, melteigite, jacupirangite, gabbro, syenogabbro, monzogabbro and monzonite. All these lithologies contain magnetite with composite, sandwich and trellis types of ilmenite intergrowths due to heterogeneous oxy-exsolution. Chromium contents of magnetite grains in the magnetite clinopyroxenite unit of the Mouding intrusion decrease from 1257 to 41 ppm within an 80 m interval, which can best be explained by the diffusion-controlled in situ crystallization in a crystal-liquid framework. Notably, magnetite grains from these alkaline intrusions are rich in Nb, Ta, Zr and Hf relative to those from subalkaline intrusions and iron oxide–apatite (IOA), iron oxide copper gold (IOCG) and porphyry deposits. This enrichment demonstrates that the high field strength elements (HFSE) are rich in the parental magmas of alkaline intrusions and have high partition coefficients between magnetite and alkaline magma. Our study demonstrates that magnetite grains in alkaline mafic–ultramafic intrusions have distinctively different trace element compositions from those in subalkaline intrusions, being useful tools in discriminating magma series and understanding the crystallization processes.