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Pegmatite-aplite systems are critical hosts for Li, Nb, and Ta mineralization, yet the role of their spatial distribution and overprinting enrichment processes remains poorly constrained. The world-class Bailongshan Li pegmatite deposit (Li2O resource >5 Mt), situated in the Western Kunlun Orogenic Belt of Northwest China, hosts Li-Nb-Ta mineralization primarily in coarse-grained spodumene pegmatites (Spd-1; >3 cm wide; pegmatite layer). These Spd-1 pegmatites are crosscut by fine-grained, spodumene-bearing pegmatites (Spd-2; <3 cm wide; aplite layer) that also exhibit distinct Nb-Ta-Sn enrichment. Two types of aplite are distinguished in the Bailongshan deposit: (1) aplite associated with and parallel to pegmatite zones, which is mostly spodumene-free, and (2) aplite layers that crosscut pegmatite zones at a small angle, exhibit a fine-grained texture, host fine-grained spodumene, and are characterized by typical hydrothermal alteration. Geochronology of columbite-group minerals (CGMs) in the coarse-grained pegmatite and fine-grained aplite layers reveals primary magmatic crystallization at ca. 210 Ma and a later metasomatic alteration at ca. 190 Ma (191.8 ± 1.5 Ma to ca. 191.0 ± 1.4 Ma), recorded by CGMs with higher Sn, Hf, Zr, and total rare earth elements (ΣREEs) with dissolution-precipitation textures. Spd-2 crystals in the fine-grained spodumene pegmatite are primarily xenocrystic, as the structural data obtained from single-crystal X-ray diffraction of both coarse-grained and fine-grained spodumene exhibits comparable structural characteristics. The electron backscatter diffraction (EBSD) data indicated a slight orientation difference (0° to 2°) between the Spd-2 grains and the larger Spd-1 crystals. Coarse-grained Spd-1 was incorporated into the fine-grained aplite layer to form the xenocrystic Spd-2; this is evidenced by their comparable crystallographic structures despite the elevated Na, Mn, Fe, Ga, and Sn concentrations in Spd-2. The “bookshelf” structures in the aplite layer further suggest that ductile deformation facilitated the mechanical disaggregation of spodumene; this, combined with metasomatic alteration, contributed to localized Nb-Ta-Sn enrichment.