Electron cyclotron resonance (ECR) has been employed to etch the surface of monocrystalline silicon (100) with sample rotation, etching effects and optical properties of low energy Ar+ beams at different ion-beam incident angles are studied. The experimental results indicate that, when ion beam energy is 1000 eV, beam current density is 265 μA/cm2, and etching time is 60 min with simultaneous sample rotation, well ordered self-organized nanodot patterns form on the Si surface. Within 0°～25°, if the incident angle increases, root mean square (RMS) of the roughness and optical transmittance of the sample are enhanced with the growth of self-organizing nano-structure, when surface roughen functions principally. If the incident angle remains increaseing, the reducing size of self-organized nanodots lessen RMS and optical transmittance of samples. If the incident angle continues to increase nearly up to 45°, the dot patterns fade away, and RMS and mean optical transmittance of samples reach the minimums of 0.83 nm and 55.05%, and the polishing effect is obvious for ion beams. If the incident angle further increases, the self-organized dot patterns appear on the sample surface again, RMS is dramatically enlarged and optical transmittance start to magnify with the angle increasing, and at about 65°, the mean optical transmittance get the maximum of 64.59%, then the RMS and optical transmittance begin to decrease slowly with the incident angle increasing. The transformation self-organized nano-structure patterns results from the interaction of spurting roughness and relaxation mechanism.