We use Sr-Nd isotopes of apatite and trace element compositions of apatite-zircon pairs from a major ore layer in each of three selected magmatic Fe-Ti-V oxide ore deposits (Hongge, Panzhihua, and Taihe) in the Emeishan large igneous province (LIP) in southwestern China to contrast the magmatic controls on ore formation. The average contents of REEs in apatite from a representative ore zone/layer in each of these deposits are higher than the predicted values of apatite crystallizing from a melt with REE contents assumed to be the same as the average values of high-Ti basalts in the Emeishan LIP, confirming that the ore-forming magmas all experienced higher degrees of fractional crystallization by major silicate minerals than the average basalt. The apatites Sm/Yb and Sr/Y indicate that the Panzhihua magma was generated at a shallower depth and experienced higher degree of plagioclase fractional crystallization than Taihe and Hongge. The apatite Sr-Nd isotopes can be reproduced by ~ 8 wt% contamination with Precambrian gneiss-schist in the parental magma for Hongge and by ~ 10 wt% and ~ 25 wt% contamination with marbles in the parental magmas for Panzhihua and Taihe, respectively. A recycled, high-T altered oceanic gabbroic component in the mantle source is a viable alternative to the marble contamination model for Taihe. Coexisting zircon trace element compositions reveal that the parental magma for Taihe (ΔFMQ+4.0) is more oxidized than those for Hongge (ΔFMQ−0.4) and Panzhihua (ΔFMQ−0.7), questioning that magma oxidation played a critical role in the genesis of Fe-Ti-V oxide ore deposits in the Emeishan LIP.