Due to the many recent Earth observation missions, very low Earth orbit (VLEO) have become a pressing topic for satellite research. Since the density of atomic oxygen (AO) in VLEO is higher than in low Earth orbit (LEO), the need for AO-resistant materials based on polyhedral oligomeric silsesquioxane (POSS) is strong. However, the effects of the side-chain groups in the POSS on AO exposure are unclear. In this study, we focused on POSS molecules modified with semifluoroalkyl groups as side chains because fluorocarbon groups, such as fluorinated ethylene propylene (FEP), are known to have high AO resistance. Semifluoroalkyl- and alkyl-substituted POSS films were fabricated and exposed to a laser-detonation AO source. Microbalance measurements showed that the mass losses of the semifluoroalkyl-substituted POSS films were larger than those of alkyl-substituted POSS films. X-ray photoelectron spectroscopy measurements showed that the silica layers formed on the semifluoroalkyl-substituted POSS were thicker than on alkyl-substituted POSS films. Surface observation using a field emission scanning electron microscope revealed microscale cracks on the surface of the semifluoroalkyl-substituted POSS. These findings indicate that POSS molecules with fluorine substituents warrant careful consideration of the AO-barrier performance of the silica layer formed during AO exposure.