The thermal dewetting behaviors of polystyrene (PS) nanocomposite thin films containing surface-modified CeO2 nanoparticles synthesized by the supercritical hydrothermal method were observed using an optical microscope. Oleic acid and decanoic acid were used as the surface modifiers of nanoparticles, and cyclohexane and toluene were used as the solvents to prepare the thin films by spin-coating. The effect of surface modifier on the dewetting morphology and the critical surface energy of the substrate below which dewetting occurred was investigated. Dewetting was more effectively suppressed by oleic acid-modified nanoparticles than by decanoic acid-modified nanoparticles. The sizes of nanoparticle aggregates on the surface of nanocomposite thin films with 10 wt% oleic acid-and decanoic acid-modified nanoparticles were observed using a scanning probe microscope. It was speculated that the difference in the dewetting behaviors of nanocomposite thin films with different surface-modified nanoparticles was due to the interaction between the nanoparticles and PS, i.e., the difference in the affinity of the surface modifier of the nanoparticles to PS.