Femtosecond laser induced darkening and permanent refractive index changes in K9 glass under different radiation conditions were experimentally studied. The micro-process of darkening generation in K9 glass was analyzed depending on the results of microscope photograph, absorption spectra, electron spin resonance spectra (ESR) and laser diffraction. It was found that hole-trapped color centers give rise to the darkening generation. Darkening and refractive index change varied with laser intensity, scan speed and line interval. Nonlinear ionization enhanced color center formation. Permanent refractive index changes were explained simply. The mechanism was still under discussion.