The Cuonadong deposit is the first large scale Sn-W-Be rare polymetallic deposit located in southern Tibet, China, where beryl is the main beryllium-bearing mineral. In this paper, the beryl crystals in the pegmatitic and hydrothermal vein orebody from the Xianglin area of the Cuonadong deposit are the research objects, marked as Beryl-I and Beryl-II, and they are investigated by EPMA, LA-ICP-MS and in situ micro-X-ray diffraction (XRD). Data by EPMA and LA-ICP-MS reveal that beryls from this area are alkaline beryls, among which Beryl-I is composed of Li-Cs beryl, and Beryl-II is composed of Na beryl and Na-Li beryl, indicating that beryls have undergone noticeable alkali metasomatism during formation. The Cs/Na ratio in Beryl-I ranges from 0.10 to 0.44, and the Mg/Fe ratio is almost 0, showing that Beryl-I is formed under high-differentiation evolution conditions and is rarely affected by hydrothermal transformation, whereas the Mg/Fe ratio in Beryl-II ranges from 2.73 to 17.31, and the Cs/Na ratio is nearly 0, indicating that Beryl-II has been obviously affected by late hydrothermal metasomatism. In situ XRD analysis shows that both Beryl-I and Beryl-II are t-beryl, and the c/a ratio of Beryl-I (1.0010–1.0012) is slightly higher than that of Beryl-II (1.0005–1.0008), which may also reflect the transition from magmatism to hydrothermal metasomatism in the late stage of pegmatitic magmatism. Based on comprehensive analysis, we believe that the precipitation of Beryl-I is mainly caused by the emplacement of highly fractionated magma containing Be to the top of the rock mass or surrounding rock, the melt-fluid undercooling, and the crystallization of volatile-bearing minerals (such as tourmaline and fluorite). Moreover, the Be-bearing ore-forming fluid has further migrated upward along the near north–south faults formed in the middle Miocene (16–15 Ma), during which Beryl-II precipitates owing to the hydrothermal water mixing, the ore-forming fluid cooling, and large amounts of crystallization of volatile-bearing minerals (mainly fluorite). Therefore, it can be concluded that beryl mineralization largely reflects the process of magmatic–hydrothermal mineralization. Because of a large number of mineralized areas with the similar metallogenic backgrounds to the Cuonadong deposit in the Himalayan region, it has great potential to be a new globally significant rare metal metallogenic belt.