Fully understanding the effect and the molecular mechanisms of plasma damage and silylation repair on low dielectric constant (low-k) materials is essential to the design of low-k dielectrics with defined properties and the integration of low-k dielectrics into advanced interconnects of modern electronics. Here, analytical techniques including sum frequency generation vibrational spectroscopy (SFG), Fourier transform infrared spectroscopy (FTIR), contact angle goniometry (CA) and X-ray photoelectron spectroscopy (XPS) have been employed to provide a comprehensive characterization of the surface and bulk structure changes of poly(methyl)silsesquioxane (PMSQ) low-k thin films before and after O<inf>2</inf> plasma treatment and silylation repair. O<inf>2</inf> plasma treatment altered drastically both the molecular structures and water structures at the surfaces of the PMSQ film while no bulk structural change was detected. For example, ∼34% Si-CH<inf>3</inf> groups were removed from the PMSQ surface, and the Si-CH<inf>3</inf> groups at the film surface tilted toward the surface after the O<inf>2</inf> plasma treatment. The oxidation by the O<inf>2</inf> plasma made the PMSQ film surface more hydrophilic and thus enhanced the water adsorption at the film surface. Both strongly and weakly hydrogen bonded water were detected at the plasma-damaged film surface during exposure to water with the former being the dominate component. It is postulated that this enhancement of both chemisorbed and physisorbed water after the O<inf>2</inf> plasma treatment leads to the degradation of low-k properties and reliability. The degradation of the PMSQ low-k film can be recovered by repairing the plasma-damaged surface using a silylation reaction. The silylation method, however, cannot fully recover the plasma induced damage at the PMSQ film surface as evidenced by the existence of hydrophilic groups, including C-O/CO and residual Si-OH groups. This work provides a molecular level picture on the surface structural changes of low-k materials after plasma treatment and the subsequent silylation repair.