The influence of the dispersion states of the nanofillers on the dewetting behavior of the polymer thin film was investigated. Polyhedral oligomeric silsesquioxanes (POSS) with various substituents were added into polystyrene (PS) thin films as the nanofillers. The dewetting rate of the films drastically changed with the surface substituents of POSS additives. Neutron reflectivity measurements indicated that the difference of the dewetting rate was associated with the dispersion state of POSS additives in the films. POSS with phenethyl groups (PhPOSS), which homogeneously dispersed into the films, resulted in the decrease of the glass transition temperature of PS and the enhancement of the dewetting of the films. POSS with a fluoroalkyl group (CpPOSS-R-f) segregated to the film surface and showed the retardation of the dewetting by the decrease of the surface energy of the film. POSS with hydroxyl groups (CpPOSS-2OH) segregated to the film surface and film-substrate interface and led to the elimination of the dewetting, suggesting the importance of the interfacial segregation for the inhibition of dewetting. These results revealed the strong relationship between the dispersion state of the nanofillers and the dewetting of the nanofilled films.