10.6 μm CO2 laser beams with different diameters are used to irradiate surface damage pits of fused silica. Experimental results show that a single pulse irradiation could repair damage pits below 50 μm efficiently, whose damage threshold could be recovered to the threshold of intact substrate. For damage with size between 50 and 300 μm, deep cracks could be efficiently repaired by using long time irradiation with low power laser before melting. It shows that laser power, irradiation time, and especially beam diameter are the main factors influencing the thermal stress distribution. However, pre-irradiation is in favor of melting crack in deep damage. After irradiation by 351 nm, 6.3 ns NdYAG laser, experimental results show that when the repair region is on the input surface, annular raised damaged region forms because of laser modulation. When the repair region is on the output surface, ablation is the main causation influencing the threshold advancement.