Fluorite of various occurrences could portray the hydrothermal metasomatism occurred in the giant Bayan Obo REE-Nb-Fe ore deposit. Two Mesoproterozoic and Paleozoic hydrothermal events with distinguished fluid origin and geochemical properties have been studied. In Mesoproterozoic, discrete fluorite from the dolomite-dominating REE-Nb ores and banded fluorite aggregates from the banded REE-Nb-Fe ores are extremely enriched in LREE and depleted in HFSE compared with the primitive mantle. In Paleozoic, fluorite from veined-breccia REE-Nb ores varies significantly in trace element components, ranging from LREE-enriched HFSE-depleted fluorite to fluorite with “flat” REE pattern and extremely depletion of Zr. The veined fluorites have variable and higher radiogenic Sr isotopic components (initial 87Sr/86Sr ratios: 0.703464–0.708208) than the discrete and banded fluorite (0.703183–0.705047), indicating crustal contamination in the Paleozoic hydrothermal fluids from Precambrian basement rocks and Bayan Obo Group. Fluorites of different occurrences and associated bastnäsite and monazite have similar Nd isotopic components and Nd evolution history, which is mostly consistent with whole rock of the ore-hosting dolomite. The Sm-Nd system of some fluorite and bastnäsite were reset during the Paleozoic alteration triggered by the closure of Paleo-Asian Ocean. In such geological setting, according to the δ34S of the dominating sulfur-bearing mineral, Paleozoic veined sulfides (∼0 ± 3‰), the prime sulfur source was oceanic crust/MORB. Relatively high δ34S of barite (∼13–14‰) was caused by fractionation of sulfur isotopes at an equilibrium temperature of 400–430 °C, rather than contribution from ancient seawater. The trace element, Sr-Nd isotope of fluorite and sulfur isotope characters of sulfides indicate carbonatitic origin of the Mesoproterozoic hydrothermal fluids, while the Paleozoic fluids, derived from subducted Paleo-Asian oceanic crust, carried sulfur components from MORB, scavenged high radiogenic Sr components from Precambrian basement rocks or Bayan Obo group, may leached a deep-seated carbonatite stock and finally altered the Mesoproterozoic mineralized ore-hosting dolomite.Both the Mesoproterozoic and Paleozoic hydrothermal fluids had initial temperature of ∼400–500 °C, and gangue minerals (fluorite, sulfide and sulfate) precipitated at the temperature of ∼320–440 °C. Preliminary thermodynamic calculations of the REE-F-C-Ca system constrained that the pressure of both fluids would not exceed 2 kbar. The drop of temperature and increase of pH are two critical factors to REE mineralization. Paragenesis of Fe-bearing minerals indicates an increase of fO2 in the Mesoproterozoic hydrothermal fluids and a drop of fS2 in the Paleozoic fluids in the Fe-O-S system. Furthermore, in the Ca-F-C-O system, the Mesoproterozoic hydrothermal fluids evolved with increasing aCa2+ and decreasing aF−, while the Paleozoic fluids present characteristic of mixing origin again with significantly variable aCa2+ and aF−.