ABSTRACT The Dahongliutan rare-metal pegmatite deposit, associated with the pegmatite dikes hosted by Dahongliutan pluton and metasedimentary rocks, is a new discovered Li–Be deposit in the the West Kunlun orogen, Northwest China. The Dahongliutan pegmatite is a classic and typical example of a highly fractionated Li-Ce-Ta (LCT) type pegmatite, with distinct regional zonation composed of well-developed garnet-tourmaline-microcline (GTM), beryl-tourmaline-muscovite (BTM) and spodumene-albite (SA) pegmatites from the barren core inward to outer zone. Detailed field studies, together with B-isotope studies of tourmaline and the chemistry of feldspar, muscovite and tourmaline, were undertaken to investigate the differentiation processes in a pegmatite magma and the different mineralizing episodes of the Dahongliutan rare-metal pegmatite deposit. Alkali metal fractionation trends (Rb, Cs and K/Rb) in the pegmatitic K-feldspar and muscovite define a primitive to evolved magmatic evolution. From low to high degrees of evolution, the mineralization stages of Dahongliutan pegmatite field are metal barren in centre, Be-rich in the intermediate and Li-rich in the outer zone. Furthermore, besides the magmatic tourmaline in the GTM pegmatite dikes, the fine-grained euhedral magmatic BTM-I type and subhedral to anhedral coarse-grained magmatic-hydrothermal BTM-II type in the BTM pegmatite dikes have been identified. The average δ11B values of the magmatic tourmalines in the GTM-type is −8.82, BTM-I type is −8.53‰, and BTM-II type is −7.85‰. Combined with petrography and chemical data, we suggest that the Dahongliutan pegmatite dikes were derived from metasedimentary source within the continental crust and the BTM-II type tourmaline is correlated with separation of an immiscible B-rich fluid during the magmatic-hydrothermal evolution. Consequently, highly fractional crystallization, albite alteration and liquid immiscibility were the main factors controlling the spatial and temporal decoupling of rare element mineralization in the Dahongliutan pegmatite deposit.