Polyurethane-urea (PU) nanocomposites containing reactive diamino-polyhedral oligomeric silsesquioxanes (diamino-POSS) and nanoclay, Cloisite 30B, were prepared via environmentally-friendly homogeneous aqueous solution polymerzation. The effect of the nanofillers (diamino-POSS and Cloisite 30B) on the viscoelastic, morphological and WAXD properties of polyurethane has been investigated as a function of concentration. For PU/POSS nanocomposite films, the microphase separation temperature of polyurethane (TMPS) was found to be concentration independent when the POSS concentration ≤6wt%; however, the TMPS shifted by about 20°C to higher temperature at 10 wt% POSS. Furthermore, the TMPS was nearly concentration independent for PU/clay nanocomposite films. TEM microphotographs confirmed that the reacted clay was exfoliated in the PU matrix while the nanoscale size of the POSS generated a finer nanoscale morphology compared to that of pure PU.