The surface density changes of the central region of the sites treated by using the CO2 laser-based non-evaporative damage mitigation for fused silica are investigated by attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR). The ATR-FTIR peak shifts of the treated sites of fused silica are monitored to determine the changes of the corresponding density. For the quenching treated sites, the surface density is increased by (0.24 ± 0.01)% compared with the initial density but the laser annealing by the exposure of a power ramp down after damage mitigation effectively suppresses the structural changes of treated sites, which could reduce the increase of the corresponding density to (0.08 ± 0.01)%. The results provide sufficient evidence that the laser annealing by a power ramp down after damage mitigation has a positive effect on the control of the structural change induced by CO2 laser-based damage mitigation.