Two series of nanostructured polyurethane with reactive diamino-polyhedral oligomeric silsesquioxanes (POSS) hybrid were synthesized via environmentally-friendly aqueous dispersions through two different methods, namely, acetone and prepolymer processes. The resulting PU/POSS nanocomposites prepared via acetone process did show more phase homogeneity compared with that of prepolymer process as confirmed by wide angle X-ray diffraction patterns of the cast films. Rheological behavior of these important classes of materials has been investigated as a function of POSS concentration and preparation method over a wide range of shear frequency and temperature. The complex viscosity and the elastic storage modulus of PU and PU/POSS nanocomposites prepared via prepolymer process were much higher than that of acetone process at a constant temperature due to the difference in the molecular weight and percentage of internal surfactant. For the PU/POSS nanocomposites prepared by the two different methods, the rheological behavior in the melt confirmed the existence of microphase separation of the hard and soft segments. The value of the microphase separation temperature (TMPS) was found to be concentration independent when the POSS concentration is ≤6wt%. For 10 wt% POSS the TMPS shifted by 20 °C to a higher temperature. The effect of POSS on the value of TMPS for prepolymer. samples is considerably different. The value of TMPS of pure PU shifted from 165 °C to 178 °C for all PU/POSS samples regardless of the concentration of POSS as measured from the dynamic heating ramps (2 °C/min heating rate at ω = 1 rad/s) of G'. The shift of TMPS to high temperature in both cases (acetone and prepolymer processes) is attributed to the large surface areas of POSS that produces relatively large interaction zones with the PU hard and soft segments.