The X-ray diffractomer, ultravidet-visible spectrophotometer and fluorescence spectrometer are used to analyze the structure, optical properties and surface defects of the α-quartz crystal before and after 10.6 μm continuous wave CO2 laser irradiation. The results show that the phase structure of the α-quartz crystal sample surface changes. The absorptivity decreases and transmissivity increases. The point defects are removed by 10.6 μm laser irradiation. During the CO2 laser irradiation, α-quartz crystal experiences a process of rapid heating and cooling. High temperature and thermal stress are the main reasons which lead to the changes of crystal structure and optical property.