Ametrine is the valuable variety in alpha quartz, and its mid-Infrared (MIR) spectra research helps to understand the differences of violet and yellow zones in amtrine. The natural and synthetic ametrine have the specific MIR absorption spectra in the violet-yellow color zones respectively. When quenched under the different temperatures, the spectra can change regularly. We conducted quench experiments of natural and synthetic ametrine using tube furnace and collected the micro MIR spectra of natural and synthetic ametrine under different quench temperature in the violet-yellow color zones. The experiments suggested that water had not direct correlation to do with the color. In sharps peak at 3 585 and 3 614 cm-1 of violet zone and broad band near 3 400 cm-1 of yellow zone, the simultaneous changes of these peaks, which occurred in same temperature, indicating that when the samples heated, the structural water may play a dominant role in change. During the heat treatment, the peaks decreased in violet zone while increased in yellow zone, that could be explained by the migration of H+ or other positive ions through the structure channels of alpha-quartz. At the same time, the research pointed out that the MIR spectra of heated yellow quartz is largely similar to the amethyst one.