Beryllium (Be), as a critical element, is an essential industrial raw material in advanced fields and the new energy industry. China is a major beryllium consumer with high external dependence, and beryllium resources are in short supply. The recently discovered Baishawo Be-Li-Nb-Ta deposit, located in the northeast of Hunan, is a large pegmatite type rare metal deposit. Previous studies show that the beryl is the dominant beryllium-bearing mineral occurring in pegmatite, whereas the occurrence state and ore-forming mechanism of beryllium are still unclear. Here, we combined field geological survey, optical microscope observation, SEM, X-ray maps, TIMA, EPMA and LA-ICP-MS analysis, to investigate the petrographic and mineralogical features of beryl, tourmaline, quartz, albite, and mica of 3# pegmatite dike in the Baishawo deposit. The results show that Be occurs not only in beryl as an independent mineral but also in tourmaline, quartz, albite, and mica as an isomorphic form. Beryl mainly distributes in the wall and intermediate zones of 3# pegmatite. The wall zone beryl is light green in color with 2 × 3 × 5 cm in size and coexists with albite, muscovite, and garnet. The beryl crystal from the intermediate zone has large grain size (~50 cm), and presents a short columnar, with longitudinal lines parallel to the c-axis on the crystal surface. The beryl from the wall zone has BeO, Li2O, and Cs2O content of 12.87%-14.01%, 0.14%-0.33%, and 0.05%-0.12%, respectively. The BeO content in beryl from the intermediate zone is 13.38%-13.96%, and the contents of Li2O and Cs2O are slightly higher than those in the wall zone, which are 0.25%-0.39% and 0.13%-0.39%, respectively. Additionally, the concentration of Be in quartz (0.20-7.13 ppm, with an average of 2.50 ppm) is lower than that of other Be-bearing minerals. Tourmaline (4.13-8.73 ppm, with an average of 5.94 ppm, The average content of Be in albite (4.74 ppm) was close to that in albite (1.22-6.98 pm, average 4.54 ppm). The content of Be in muscovite (16.9-53.8 ppm, average 21.77 ppm) was the highest, with up to 53.8 ppm. It is considered that the 3# pegmatite dike belongs to LCT (Li-Cs-Ta) pegmatite and is of granitic melt crystallization differentiation origin for wall zone pegmatite, while the pegmatite in the intermediate zone is in the magmatic-hydrothermal transition stage, which is subject to the metasomatism of late hydrothermal fluid. In the Baishawo deposit, beryl coexists with alkaline feldspars such as albite, and the BeO contents is up to 13.44%, which has a significant industrial value and can be used for green selection and smelting by acid flotation. This study provides a reference for the occurrence and genesis of beryllium in rare metal pegmatite deposits, and also a scientific basis for the exploration, development, evaluation, and prediction of beryllium resources in rare metal pegmatite deposits.