Abstract: ECR was employed to etch the surface of monocrystalline silicon(100), etching effects and optical properties of low energy Ar+ ion beams with different ion energies and fluxes under normal ion incidence were studied. The experiment results indicate that, when ion flux density was 88-310 A/cm2 with ion beam energy of 1 000 eV, self-organizing nano dot structure appeared on the sample surface, orderly arrangement of the micro-structure was along with the increase in ion flux density; RMS decreased until the flux density was near 160 A/cm2, and then increased rapidly; The average transmittance of etched sample, within the range of near-infrared bands, was improved from 53% to more than 57%, which enlarged with the increase in orderliness of self-organizing nano-structure. When ion beam energy was 500-1 000 eV with ion flux density of 270 A/cm2, the tiny nano dot structure gradually formed, which tended to be concentrated and orderly with the increase of ion beam energy. If ion energy was going up below 1 100 eV, RMS slowly increased but rapidly reduced over the number. The transmittance of etched sample was sharply improved, with the increasing orderliness of self-organizing nano-structure. Etching rate was directly proportional to the square of ion flux energy. The pattern transformation of self-organizing nano-structure results from the interaction of spurting roughening and relaxation mechanism.