The Yinachang deposit in the Kangdian region, Southwest China, contains large amounts of Fe, Cu and REE, and formed at ∼1700Ma. In this deposit, there are three stages of alteration and mineralization, including pre-ore Na–(Fe) alteration, Fe–(REE) mineralization, and Cu–(REE) mineralization. In the Fe–(REE) mineralization stage, REE-rich fluorapatite, with total REE concentrations ranging from 10,700 to 34,000ppm, formed together with magnetite. In the following Cu–(REE) mineralization stage, large amounts of REE, especially LREE, were leached out of the REE-rich fluorapatite due to the interaction between fluorapatite and Cl-, F-, CO2-, and Ca-rich, but REE-unsaturated fluids. The leaching of REE was associated with the removal of Si, Na, Th, U, Pb, and Ba, and modification of the oxygen isotope signature in the fluorapatite.During a ∼840Ma tectonothermal event, REE-rich fluorapatite underwent the second interaction with oxidized, F-, CO2-, and possibly Cl-rich, but Na- and Ca-deficient fluids. Due to fluid–fluorapatite interaction, REE were removed from the fluorapatite, but were immediately reincorporated into new phases within the fluorapatite. Thus, the altered fluorapatite contains abundant REE mineral inclusions, including bastnäsite-(Ce), monazite-(Ce), and minor xenotime-(Y). A very small portion of the LREE were transported out of the fluorapatite, and formed bastnäsite-(Ce) and monazite-(Ce) grains in the vicinity of the altered fluorapatite.In addition to the metasomatism of fluorapatite, allanite and “primary” synchysite-(Ce) from the Cu–(REE) mineralization stage were also altered with variable replacement of allanite by an assemblage of synchysite-(Ce)+chlorite±bastnäsite-(Ce) and “primary” synchysite-(Ce) by bastnäsite-(Ce). These styles of alteration were possibly synchronous with the second alteration phase of the fluorapatite.This study demonstrates that REE can be mobilized during multiple stages of hydrothermal activities and highlights the significant controls fluid compositions have on REE transportation and deposition in hydrothermal system.