The Bayan Obo associated fluorite deposit is a super-large deposit attracting worldwide attention, but the genesis of the deposit is still controversial. Based on the systematic study of the geological characteristics and the distribution of fluorite-bearing ores in the western Bayan Obo mine, the geochemical study of trace and rare earth elements of fluorite deposit and ore-bearing H8 dolomite is carried out in this paper. The results show that the fluorite deposit in the western mining area belongs to the dolomite-type ore. The REE characteristics of both fluorite and dolomite are relatively enriched in LREE and relatively depleted in HREE. The REE distribution patterns of fluorite and dolomite have similar synchronization. The contents of Ba, Th, Sm and Ce in all samples are relatively high, especially the contents of Ba and Th are obviously high. The δEu values of fluorite ores in the mining area range from 0.93 to 1.14, with both positive and negative anomalies. The δCe values range from 1.15 to 2.11, with an average of 1.51, showing positive anomalies of Ce.Based on the geological characteristics of fluorite deposit, trace and rare earth elements and plots of (Y+La)-Y/La, La/Ho-Y/Ho and Tb/Ca-Tb/La, combined with previous studies on fluid inclusions in fluorite, it is concluded that the associated fluorite deposit in the western Bayan Obo mine belongs to medium-high temperature, hydrothermal metasomatism type fluorite deposit. Different from typical sedimentary-reworked and hydrothermal filling fluorite deposits in China, the genesis of the deposit has nothing to do with intrusive granite, and the main ore-forming materials of F and Ca elements are derived from the metasomatism of early mafic carbonate rocks by medium-high temperature fluids derived from caledonian calcareous carbonate rocks.