Abstract The Yichun Ta-Sn-Li deposit occurs within the 9.5-km2 Yashan Igneous Complex, which is made up of felsic, peraluminous intrusions including two-mica, Li-mica, and topaz-lepidolite granites. The topaz-lepidolite granite forms a thin sheet confined to the upper part of the Li-mica granite and is separated from the host metasediments by a marginal pegmatite. The topaz-lepidolite granite is characterized by the presence of snowball textures in which quartz, K-feldspar, and topaz phenocrysts contain albite laths and rare lepidolite and columbite arranged along growth zones. These textures indicate simultaneous crystallization of these phases and attest to the subsolvus character of the topaz-lepidolite granite. Minor and accessory phases in the topaz-lepidolite granite include amblygonite, cassiterite, columbite-tantalite, microlite, wodginite, zircon, monazite, and pollucite. The topaz-lepidolite granite is characterized by low SiO2 (68.6–69.7 wt %), TiO2 (0.01 wt %), Fe2O3(total) (0.15–0.33 wt %), MgO (0.01–0.05 wt %), and CaO (0.15–0.19 wt %), whereas Al2O3 (17.97–18.26 wt %), Li2O (0.90–2.09 wt %), P2O5 (0.43–0.54 wt %), and F (1.09–2.30 wt %) are all very high. Na2O ≫ K2O due to both high Na2O (5.18–6.30 wt %) and low K2O (2.63–3.05 wt %). The topaz-lepidolite granite contains extremely high concentrations of Rb (>3,300 ppm), Cs (>340 ppm), Sn (>140 ppm), and Ta (>120 ppm), with very low Zr/Hf and Nb/Ta. Gaps of >3.5 wt % SiO2 and >2.5 wt % Al2O3 together with large increases in F, Li2O, and P2O5 between the Li-mica and topaz-lepidolite granites are not compatible with an evolution by Rayleigh fractionation processes. It is proposed instead that early crystallization of the Li-mica granite led to the formation of an Si-poor, Al-, Na-, and flux-rich boundary layer whose low viscosity and density allowed effective separation from the remaining melt and crystals. This melt concentrated incompatible elements including tin and tantalum and accumulated in the upper part of the magma chamber where it crystallized the sheet-like bodies of marginal pegmatite and topaz-lepidolite granite. The uppermost part of the topaz-lepidolite granite consists of aplite and overlying quartz lepidolite rock, which is composed mainly of quartz, lepidolite, albite, K-feldspar, topaz, amblygonite, cassiterite, and columbite. Compared to the topaz-lepidolite granite the aplite and quartz-lepidolite rock shows a number of complementary element enrichments and depletions. The quartz-lepidolite rock is enriched in Fe, Mn, K, Rb, Cs, Li, F, Ba, Sr, Ti, Zr, Nb, W, Th, and Sm. The formation of the quartz-lepidolite rock is interpreted to result from separation of an F- and Li-rich alkaline phase, which accumulated beneath the already crystallized marginal pegmatite. Complementary to this was crystallization of the strongly peraluminous sodic aplite with the highest tantalum contents measured in this study.