Electron cyclotron resonance ion source has been employed to erode the surface of sapphire (crystal orientation A) and the self-organized nanostructures induced by Kr+ ion beam on sapphire surface at different incident angles are researched. The surface of the sapphire sample was etched at different incident angles using a plasma and ion beam etching equipment. The etching rate and surface morphology of the sapphire samples were analyzed by Taylor Surf CCI2000 non-contact surface measuring instrument and atomic force microscope. The experimental results indicate that, with the ion beam energy 400 eV, the accelerator voltage 200 V, and beam current density 310 μA/cm2, the ordered punctate nanostructures with small longitudinal dimension appear on the surface of the sapphire sample at small angle incidence; the increase of incident angle will obtain stripe-like nanostructure on the sample surfaces; when the incident angle continues to increase up to 30°, short-range order and stripe-like structures appear on sample surfaces with an aspect ratio of 0.87; the incident angle continues to increase and the vertical height decreases until the nanostructures disappear; when the angle reached 60°, stripe-like structures appear on sample surfaces again, and at 70°, short-range order and stripe-like structures with an aspect ratio of 1.07 are formed. The formation of self-organized nanostructures first appear in the form of "island", and then the stripe-like nanostructures are grown on the island. Eroding time extension is unable to change nanostructure topographies, but able to increase the vertical nanostructure dimensions and enhance the orderliness.