The friction and tribochemical wear of native oxide (SiOx) layers formed on a silicon surface were investigated with atomic force microscopy using a silica (SiO2) sphere tip in ambient air (50% relative humidity). The native SiOx layer thickness was determined to be similar to 0.8 nm with auger electron spectroscopy. The oxide-free Si/H terminated silicon surface was also studied as a reference for comparison. It was found that friction is higher on the Si/SiOx surface than the Si/H surface; but, the wear of the Si/H surface occurs much more readily than that of the Si/SiOx surface when wear depth is less than the thickness of native oxide layer on Si/SiOx surface (similar to 0.8 nm). Based on attenuated total reflection infrared spectroscopy analysis, the friction appears to be governed by the thickness and structure of the adsorbed water layer. Although the wear process in humid conditions is through tribochemical reactions involving the adsorbed water, the removal rate of the substrate layer varies depending on the effective activation energy. These findings are important for the tribological design of silicon-based micro/nanodevices working in humid ambience.