There is a strong controversy about the petrogenesis of tourmaline nodules and their relationship with coeval tourmaline-bearing granites, which are commonly associated with magmatic-hydrothermal rare metal deposits (e.g., Sn, Nb, and Ta). In this study, tourmaline is extensively distributed in tourmaline-bearing nodules (NT-type), pegmatite (PT-type), and fine-grained granitic dyke (GT-type), which are hosted by the Late Cretaceous Nattaung biotite granite (Myanmar). Zircon UPb dating results (~71 Ma) indicate that PT- and GT-types tourmaline-bearing magmatic rocks formed synchronously with biotite granite. All tourmalines have alkali group and schorl composition with Mg/(Mg + Fe) ratios of 0.03–0.45 and Na/(Na + Ca) ratios of 0.73 to 1.00. NT-type tourmaline shows high Nb/Ta ratios and V and Sr contents, indicating that they were likely crystallized from B-rich melts early immiscible with less evolved granitic magmas. PT- and GT-type tourmalines probably formed in aggregated B-rich melts that continuously separated from more evolved granitic magma, supported by their low Nb/Ta ratios and V and Sr contents. In addition, the studied tourmaline displays a slight variation of B isotopic compositions (δ11B values ranging from −12.2 ± 0.7‰ to −14.9 ± 0.4‰), likely resulted by Rayleigh fractionation of tourmaline. Their light B isotopic values are consistent with those of average continental crust, also revealing that the Nattaung granite was mainly derived from partial melting of the ancient Sibumasu crust. Importantly, late-stage PT- and GT-type tourmalines have higher Sn, Zn, Nb, and Ta contents than early-stage NT-type tourmaline, suggesting that the evolved B-rich magma could be one precursor to produce Sn-Nb-Ta-Zn deposits associated with extensive tourmaline in the world.