Geochemical variations of Na- and Cs-rich beryl were studied in the Koktokay #3 pegmatite, Altai district, China. Complex internal textures in individual crystals characterize two groups of beryl (primary and secondary). Complete analyses of the primary beryl reveal a broad range of alkali contents (mostly Na and Cs) and femic contents (mostly Fe) between outer (I–IV) and inner (V–VII) zones of the pegmatite. Primary beryl in outer zones contains 0.16–0.92 wt% FeO, 0.39–1.87 wt% Na2O and ~0–0.43 wt% Cs2O, respectively, whereas that in inner zones contains negligible FeO but higher alkalis with 1.19–1.99 wt% Na2O and 2.99–3.95 wt% Cs2O. Three types of secondary beryl can be distinguished. (1) The first is the Cs-enriched veinlets with up to 8 wt% Cs2O and 2.2 wt% Na2O in primary beryl from the zones I–IV, which resulted from precipitation of Cs-rich fluids along fractures in primary beryl crystals. (2) The second type is a mosaic-like texture consisting of a Cs–Na-poor domain and Na-Cs-rich veinlets within primary, blocky beryl crystals. Textural relationship indicates a two-step hydrothermal alteration. (3) The third is Na-enriched beryl that occurs as a marginal zone of primary beryl or as network of veinlets in primary beryl, and is simply related to hydrothermal replacement of primary beryl by Na-rich fluids.