The Pingchuan iron deposit, located in the Yanyuan region of Sichuan Province, SW China, has an ore reserve of 40 Mt with ~ 60 wt% Fe. Its genesis is still poorly understood. The Pingchuan iron deposit has a paragenetic sequence of an early Fe-oxide–Pyrite stage (I) and a late Fe-oxide–pyrrhotite stage (II). Stage I magnetite grains are generally fragmented, euhedral–subhedral, large-sized crystals accompanying with slightly postdated pyrite. Stage II magnetite grains are mostly unfragmented, anhedral, relatively small-sized grains that co-exist with pyrrhotite. Combined with micro-textural features and previously-obtained geochronological data, we consider that these two stages of iron mineralization in the Pingchuan deposit correspond to the Permian ELIP magmatism and Cenozoic fault activity event. Both the Stage I and II magnetites are characterized with overall lower contents of trace elements (including Cr, Ti, V, and Ni) than the ELIP magmatic magnetite, which suggests a hydrothermal origin for them. “Skarn-like” enrichment in Sn, Mn, and Zn in the Stage I magnetite grains indicate significant material contributions from carbonate wall-rocks due to water–rock interaction in ore-forming processes. Stage II magnetite grains contain higher Mn concentrations than Stage I magnetite grains, which possibly implies more contribution from carbonate rocks. In multiple-element diagrams, the Stage I magnetite shows systematic similarities to Kiruna-type magnetite rather than those from other types of deposits. Combined with geological features and previous studies on oxygen isotopes, we conclude that hydrothermal fluids have played a key role in the generation of the Pingchuan low-Ti iron deposit.