Helium ion implantation in the sol-gel silica films was conducted at different fluences to study the impact of ion irradiation on defects, microstructures, wettability, optical properties and laser damage performance. The damage mechanism and performance degradation of the films induced by helium ion irradiation were analyzed. The cracks are observed after ion implantation and their transverse size increases but the depth decreases with the increase of ion fluence. At the same time, many small pores appear on the film surface and further expand at larger ion fluence. The Si–O–Si bond length and bond angle are reduced by helium ion implantation, thus leading to the densification of silica films. Helium ion implantation causes Si–Si bonds and Si–O bonds to break to form the defects such as ODCs and NBOHCs, further transforming into E′ centers. After ion implantation, the film surface changes from hydrophobic to hydrophilic due to the reduction of –CH3 groups, thus degrading the anti-pollution performance of the film. The significant decreases of laser damage thresholds of silica films are resulted from the increase of E′ centers and the expansions of cracks and pores. The results provide a reference to evaluate the lifetime of silica films used in high-power laser facilities, which is very important for the research of inertial confinement fusion.