The Cuonadong Sn–W–Be polymetallic deposit in the Himalayan leucogranite belt is a representative hydrothermal deposit. The role of fluid exsolution directly from magma and the fluid reaction with surrounding rocks for ore-forming element enrichment is still controversial. Tourmaline is a significant B-bearing mineral in the hydrothermal deposit, and its geochemical and B isotopic signatures can record the source and evolution of the ore-forming fluid. Two types of hydrothermal tourmaline in the hydrothermal quartz vein (Tur-1) and skarn (Tur-2) were used in this study. Both Tur-1 and Tur-2 have low X-site occupancy and mainly belong to the alkali group. Tur-1 plots in the schorl field, whereas Tur-2 is largely Mg-rich dravite. The B isotope analyses of Tur-1 have δ11B values of −13.7 to −13.2‰, whereas Tur-2 has higher δ11B values of −11.1 to −9.3‰. The distinct contact relationship and geochemical compositions suggest that Tur-1 in the hydrothermal vein was formed from a magmatic-hydrothermal fluid with little influence from surrounding rocks and had a genetic relationship with the Cuonadong leucogranite, whereas Tur-2 in the skarn involved more fluid from surrounding rocks with high δ11B values and strong metasomatic texture. The higher ore-forming element contents in Tur-2 than those in Tur-1 indicate that the reaction between the magmatic exsolution fluid and the surrounding rock is essential for the enrichment and precipitation of ore-forming elements.