The Bayan Obo REE-Nb-Fe deposit, which reserves the current largest REE resources globally, also hosts over 70% of China's Nb resources. Unlike many world-class carbonatite-related Nb deposits (e.g. Morro dos Seis Lagos and Araxa, Brazil) with igneous or secondary origin, Nb was mainly stored in Nb-bearing minerals (aeschynite, ilmenorutile, baotite, fergusonite etc.) of hydrothermal origin at Bayan Obo, supported by evidence from petrography, element and isotopic geochemistry. Although igneous fersmite and columbite were occasionally discovered in local carbonatite dykes, the Mesoproterozoic and Paleozoic hydrothermal metasomatism occurred in the ore-hosting dolomite, related to carbonatite intrusion and the closure of Paleo-Asian Ocean respectively, has played a more significant role during the ultimate Nb enrichment. REE, however, was significantly enriched during both the carbonatite-related magmatic and hydrothermal processes. Consequently, there was differentiated mineralization between REE and Nb in the carbonatite dykes and the ores. Niobium mineralization at Bayan Obo is rather limited in Mesoproterozoic carbonatite, whereas more extensive in the metasomatized orehosting dolomite, and generally postdating the REE mineralization at the same stage. According to mineral geochemistry, Bayan Obo aeschynite was classified into 3 groups: aeschynite-(Nd) with convex REE patterns (Group 1); aeschynite-(Ce) (Group 2) and nioboaeschynite (Group 3) with nearly flat REE patterns. Aeschynite (Group 1), ilmenorutile and fergusonite precipitated from Paleozoic hydrothermal fluids with advanced fractionation of Ce-rich REE minerals. The Mesoproterozoic hydrothermal Nb mineralization, represented by aeschynite (Group 3) and baotite, occurred postdating REE mineralization at same stage. Besides, fersmite and aeschynite (Group 2) precipitated from the Mesoproterozoic REE-unfractionated melt and hydrothermal fluids, respectively. All above Nb-bearing minerals exhibit extreme Nb-Ta fractionation as a primary geochemical characteristic of mantle-derived carbonatite. The forming age of the aeschynite megacrysts (Group 1) has not been accurately determined. However, the potential age was constrained to similar to 430 Ma or alternatively similar to 270-280 Ma subjected to subduction and granite activity, respectively. These aeschynite crystals inherited REEs from multiphase former REE mineralization, with an intermediate apparent Sm-Nd isochron age between the Mesoproterozoic and the Paleozoic REE mineralization events.