A molecular dynamics simulation approach was adopted to investigate the domain microstructure of polyurethane (abbreviation PU) hybrid composites with trisilanolisobutyl polyhedral oligomeric silsesquioxane (abbreviation TSI-POSS) covalently bonded to polymer chains. The accuracy of models and force field has been verified by wide-angle X-ray scattering and volume-temperature behavior analysis. TheWAXS results indicate that with TSIPOSS concentration increasing in PU hybrid composites, distinct crystallite clusters are formed which increase the volume of hard segments and lead to the microphase separation. Furthermore, details of chain packing have been evaluated by radial distribution function, which shows that below 13wt% TSI-POSS concentration, the number of contacts between neighboring chains is decreased due to the prominent cage of TSI-POSS. However, when TSI-POSS concentration is up to 22wt%, the number of contacts is increased because the formation of crystallite cluster pulls neighboring chains closer to each other and significantly shortens their distance. The mobility of the TSI-POSS cores and PU composite backbones has been determined by the mean square displacement. The result reveals that the incorporation of TSI-POSS as the rigid core in the polymer backbone apparently restricts motions of the surrounding chains, which is also supported by volume-temperature behavior analysis as the glass transition temperature of PU composites increases with rising TSI-POSS concentration.