Tourmaline is an important functional and gem material. The current study examines pink, green, and brownish-green tourmalines from Altay deposit. Based on X-ray fluorescence (XRF) quantitative analyses and ultrariolet-visible-near-infrared (UV-VIS-NIR) spectral analyses in combination with annealing experiments, the color center of tourmaline is found to be related to the d-d transitions of ions or the d-d transitions of exchange coupled ions. Annealing treatment affects the color improvement of tourmaline crystals.