This study, conducted a spectroscopic analysis of 10 gem-quality blue tourmaline samples from Minas Gerais, Brazil, focused on detailed variations in their infrared, Raman, and UV-VIS spectra. Conventional gemological tests, electron-probe microanalysis, infrared spectroscopy (mid- and near-infrared), Raman spectroscopy, and UV-visible spectroscopy were used to systematically analyze the chemical composition and spectral characteristics of the samples. The infrared spectra revealed vibrations of [YO6], [TO4], [BO3], [OH], and H2O groups, indicating different bonding profiles, with the [OH] vibrational frequency showing a direct correlation with FeO and MnO content. The Raman spectra primarily reflected the stretching vibrations of metal–oxygen bonds and hydroxyl groups, indicating the complexity of the local environment in the crystal structure. The UV-VIS spectra showed that the broad absorption band around 725 nm was due to intermetallic charge transfer between Fe2+ and Fe3+. This work provides new insights into the local bonding environment within the crystal structure by providing precise spectral data of natural blue tourmaline, and a more accurate classification and evaluation of blue tourmaline through fine spectral change characteristics related to crystal chemistry has important implications for both academic research and the gemstone industry.