To improve the laser induced damage thresholds of high power laser films, the effects of directional ion cleaning on the characteristics of substrate surface were investigated. Using End-Hall ion source, K9 glass substrates were cleaned under different cleaning parameters. The re-contaminated phenomenon and ion cleaning effect were verified by optical microscope. The contact angles of substrates before and after ion cleaning were measured using a contact angle analyzer. Atomic force microscopy (AFM) and profile meter were used to measure the substrate pattern and roughness before and after ion cleaning with different parameters, respectively. After ion cleaning, the mechanisms of substrate surface characteristics modification e.g. cleanness, surface energy, contact angle, surface roughness and surface topography were analysed. The investigation shows that directional ion cleaning can remove the re-contaminated impurity, increase the surface energy, control the roughness and pattern of surface, and it is an efficient substrate surface processing method to improve the characteristics of substrate.