Tourmaline gemstones have an extremely complex composition and show great variety in color. Most color centers are related to transition-metal ions. Oxidation/reduction of these ions is known to be related with the color enhancement of tourmaline caused by gamma-ray (γ)-irradiation and/or thermal treatment. However, the current understanding of the microscopic structure of the color centers remains weak. In this work, γ-irradiation was performed on three types of tourmaline gemstones to enhance the colors of the gemstones: two pink from Afghanistan and one green from Nigeria. All three samples were irradiated at 600 and 800 kGy. Their crystal structural and chemical behaviors have been investigated by using a Rietveld refinement analysis of neutron diffraction data, Energy Dispersive X-ray Fluorescence (EDXRF), Ultraviolet-visible Spectroscopy (UV-Vis) and X-ray Photoelectron Spectroscopy (XPS), and the results were compared with data obtained for samples in the natural state. Pink tourmaline of a high number of Mn ions (T2, 0.24 wt%) showed significant improvement in the quality of the pink color (rubellite) after irradiation of 800 kGy while the pink tourmaline of low MnO content (T1, 0.08 wt%) showed color adulteration. Pink color enhancement in T2, responding to darker pink, was associated with increases in the two absorption bands, one peaking at 396 and the other at 522 nm, after irradiation. These absorption bands are ascribed to d-d transitions of divalent manganese. T1 with color enhancement due to oxidation of Mn2+ showed a slightly larger <Y-O> distance. The green tourmaline containing much higher amounts of both Mn (T3) and Fe ions, 2.59 wt% and 5.7 wt%, respectively, changed to a yellow color after irradiation at 800 kGy. The refined structural parameters of this sample revealed distortions in the Z site. The <Z-O> distance decreased from 2.033 to 2.0192 Å. In addition, the unit-cell parameter was decreased after irradiation. The color change in T3 is ascribed to a decrease in the absorption band’s intensity in the red color region (600 ∼ 750 nm). XPS measurement results also supported that the relative ratios of the Fe2+/Fe3+ [Fe3+ (Fe2p 3/2 711.2 and Fe2p 1/2 724.3 eV), Fe2+ (Fe2p 3/2 710.2 and Fe2p 1/2 722.8 eV)] and Mn2+/Mn3+ [Mn2+ (Mn2p 3/2 641.4 and Mn2p 1/2 652.3 eV), Mn3+ (Mn2p 3/2 641.9 and Mn2p 1/2 653.3 eV)] peak intensities were decreased after irradiation.