Nanocomposites prepared by incorporating functionalized polyhedral oligomeric silsesquioxane (POSS) into polymer matrices afford a wide range of versatile hybrid materials for use in technologies ranging from cosmetics and pharmaceuticals to sensors and batteries. Here, we investigate the phase behavior of nanocomposites composed of poly(ethylene oxide) (PEO) and monosubstituted isobutyl POSS (iPOSS) modified with different functional moieties. Microscopic analyses of blends containing these iPOSS variants reveal the existence of different macroscopic morphologies and surface topologies. In the presence of octa-iPOSS, a POSS-rich surface cell motif reminiscent of breath patterns develops, whereas addition of allyl-iPOSS promotes the formation of surface plates. While aminopropyl-iPOSS forms dispersed aggregates, maleamic acid-iPOSS disperses in PEO with little effect on PEO crystal morphology. We perform rotational isomeric state Monte Carlo simulations to discern the effect of monosubstitution on the interaction energy between iPOSS and PEO, and establish the molecular-level origin for these observed differences in phase behavior.