Currently, it has been confirmed that the ore-hosting dolomite of the giant Bayan Obo deposit is the Mesoproterozoic igneous carbonatite, but the roles, that the Paleozoic tectonothermal events played, are still poorly understood. In this study, we present a comprehensive investigation on the geochemistry of various carbonates to understand the generation of the Bayan Obo carbonatite. Hydrothermal monazite Th-Pb dating (peaking at ∼ 420 Ma) identified an atypical coarse-grained dolomite, which occurring as veins, and cutting through typical fine dolomitic facies. Typical coarse dolomitic facies and atypical coarse-grained dolomite are significantly different in terms of MgO, FeO, MnO, Y, Al, Si, V, Ti, Ni, Sc, and ∑REE contents and the C-O-Sr isotopic compositions, and atypical coarse-grained dolomite has lower Ba and Sr contents, lower Co/Ni ratio, with strong Eu positive anomaly and more scattered element concentration, suggesting that it has a different origin from typical coarse dolomitic facies, crystallizing from a relatively low-temperature and oxidized environment. The pervasiveness of magma flow structure and magnetite mass in the contact zone between the granite plutons and the fine dolomitic facies indicates that, at ∼ 270 Ma, the heat flux from granitic magma triggered melting of the fine dolomitic facies, forming remelted calcitic carbonatite. In addition, Th-Pb ages of monazite ranging from 1350 Ma to 240 Ma and the REE-poor properties of both remelted carbonatites suggest that both Paleozoic thermal events only caused REE activation and redistribution, without introducing additionally exogenous ore-forming metals. Accordingly, we propose that the dolomite mass in Bayan Obo are Mesoproterozoic mantle-derived carbonatites (including ore-hosting dolomite and carbonatite dike), which underwent remelting at ∼ 440 Ma and ∼ 270 Ma, respectively.