SiO2 thin films are widely used in micro-electro-mechanical systems, integrated circuits and optical thin film devices. Tremendous efforts have been devoted to studying the preparation technology and optical properties of SiO2 thin films, but little attention has been paid to their mechanical properties. Herein, the surface morphology of the 500-nm-thick, 1000-nm-thick and 2000-nm-thick SiO2 thin films on the Si substrates was observed by atomic force microscopy. The hardnesses of the three SiO2 thin films with different thicknesses were investigated by nanoindentation technique, and the dependence of the hardness of the SiO2 thin film with its thickness was analyzed. The results showed that the average grain size of SiO2 thin film increased with increasing film thickness. For the three SiO2 thin films with different thicknesses, the same relative penetration depth range of ~0.4–0.5 existed, above which the intrinsic hardness without substrate influence can be determined. The average intrinsic hardness of the SiO2 thin film decreased with the increasing film thickness and average grain size, which showed the similar trend with the Hall-Petch type relationship.