Thin native oxide films on Si(100) have been previously shown to be decomposed by exposing the film surface to synchrotron radiation (SR) in the vacuum‐ultraviolet region. In this study, photoemission and photon‐stimulated desorption (PSD) experiments are performed to investigate the synchrotron‐radiation‐induced decomposition of a native oxide film on Si(100). For mass analysis of the PSD ions, the time‐of‐flight method is utilized. Si 2pcore‐level and valence‐band photoemission spectra demonstrate that the native‐oxide decomposition preferentially takes place on the thin parts of the native oxide film which are terminated with Si—OH and Si—H bonds. It is shown that the native‐oxide decomposition is accompanied by desorption of H+and O+ions. The H+PDS ion yield decreases exponentially with increasing the exposure time of SR, whereas the O+PSD one first increases with the exposure time, and subsequently decreases with the exposure time after the H+PSD ion yield substantially drops. The behavior of the O+PSD ion yield is explained in terms of the photon‐induced Si—O bond breaking reaction promoted by removing surface hydrogen atoms through the H+PSD process in which a Si—H bond and the O—H bond in a Si—OH bond are ruptured.