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Electron cyclotron resonance ion source has been employed to etch the surface of sapphire (C-cut), introducing metallic stainless steel impurities to investigate the evolution law and optical properties of the self-organized nanostructure on the sapphire surface at different target distances. The atomic force microscope was used to observe the morphological changes of the sample surface, the Taylor Surf CCI 2000 white light interference surface measuring instrument was used to measure the surface roughness; X-ray photoelectron spectroscopy was selected to characterize the chemical composition. The experimental results indicate that, with the ion beam energy of 1000 eV, the beam current density of 487 μA/cm2, the oblique incident angle of 65°, and the erosion duration of 60 min, the distance between the sapphire sample and the impurity target increases from 1 cm to 4 cm, island-like structures appear on the sample surface and gradually evolve into continuous ripple structures. At the same time, as the target distance increases, the orderliness of the self-organized nanostructures enhances, the longitudinal height gradually decreases, while the spatial frequency is unchanged. There are very few metal impurities on the etched sample surface. The appearance of microstructures has antireflection effect on sapphire. During the ion beam sputtering process, island-like structures promotes the growth of ripple nanostructures but destroys orderliness.