Optical properties (transmission and refractive index) and phase change (from amorphous to crystal) of a commonly used glass, quartz, were investigated before and after focused ion beam (FIB) bombardment with ion energy from 30 to 50 keV. We found different influences of FIB bombardment on the optical properties and chemical structure of the quartz in the wavelength region of visible and near infrared, respectively. The quartz still can be used in the infrared wavelength for conventional optical applications. As an application example, an array of diffractive optical elements (DOEs) was directly fabricated on the quartz by the FIB milling. The measured diffraction efficiency of the DOEs is 83.5%, which is acceptable for practical use.