The laser damage resistance of fused silica optics depends significantly on the surface quality. In this work, anisotropic etching with inert ion beams at various ion incident angles was performed to investigate the evolution of the fused silica surface. The results show that the surface is smoothed when the incident angle is below 30∘30∘. However, the fused silica surface starts to become coarse owing to the formation of nanostructures on the surface when the incident angle exceeds 30∘30∘. Further, ion beam etching at a large incident angle of 70∘70∘ removes subsurface defects and less induces nanostructures, resulting in reduction of the surface roughness. The concentrations of impurities and defects are both significantly reduced after ion beam etching. The surface quality, subsurface and surface defects, and surface impurities determine the variation in the laser damage threshold of fused silica with the ion incident angle. The results demonstrate successful application of ion beam etching to improve the laser damage resistant characteristics of fused silica optics. Ion beam etching is a very versatile tool that provides physical erosion to anisotropically mitigate surface damage of fused silica.