Owing to the superimposition of water-rock interaction and external fluids, magmatic source signatures of ore-forming fluids for vein-type tin deposits are commonly overprinted. Hence, there is uncertainty regarding the involvement of magmatic fluids in mineralization processes within these deposits. Tourmaline is a common gangue mineral in Sn deposits and can crystallize from both the magmas and the hydrothermal fluids. We have therefore undertaken an in situ major, trace element, and B isotope study of tourmaline from the Yidong Sn deposit in South China to study the transition from late magmatic to hydrothermal mineralization. Six tourmaline types were identified: (1) early tourmaline (Tur-OE) and (2) late tourmaline (Tur-OL) in tourmaline-quartz orbicules from the Pingying granite, (3) early tourmaline (Tur-DE) and (4) late tourmaline (Tur-DL) in tourmaline-quartz dikelets in the granite, and (5 and 6) core (Tur-OC) and rim (Tur-OR), respectively of hydrothermal tourmaline from the Sn ores. Most of the tourmaline types belong to the alkali group and the schorl-dravite solid-solution series, but the different generations of magmatic and hydrothermal tourmaline are geochemically distinct. Key differences include the hundredfold enrichment of Sn in hydrothermal tourmaline compared to magmatic tourmaline, which indicates that hydrothermal fluids exsolving from the magma were highly enriched in Sn. Tourmaline from the Sn ores is enriched in Fe3+ compared to the hydrothermal tourmaline from the granite and displays trends of decreasing Al and increasing Fe content from core to rim, relating to the exchange vector Fe3+Al–1. This reflects oxidation of fluids during the interaction between hydrothermal fluids and the mafic-ultramafic wall rocks, which led to precipitation of cassiterite. The hydrothermal tourmaline has slightly higher δ11B values than the magmatic tourmaline (which reflects the metasedimentary source for the granite), but overall, the tourmaline from the ores has δ11B values similar to those from the granite, implying a magmatic origin for the ore-forming fluids. We identify five stages in the magmatic-hydrothermal evolution of the system that led to formation of the Sn ores in the Yidong deposit based on chemical and boron isotope changes of tourmaline: (1) emplacement of a B-rich, S-type granitic magma, (2) separation of an immiscible B-rich melt, (3) exsolution of an Sn-rich, reduced hydrothermal fluid, (4) migration of fluid into the country rocks, and (5) acid-consuming reactions with the surrounding mafic-ultramafic rocks and oxidation of the fluid, leading to cassiterite precipitation.