Nanoscale and crystalline morphology of TPU nanocomposites bearing MMT and laponite clays were studied. Laponite was dual modified using ionic and covalent modifications by different silanes. TPU-clay nanocomposites having variegated modified clays, prepared by solution casting, were characterized using TEM, SAXS, variable temperature XRD (VTXRD), and MDSC. TEM show the uniform clay dispersion in MMT nanocomposites as compared to laponite composites. SAXS showed satisfactory fitment of Guinier eqn. at lower q values. Fitment of Porod eqn. is inferior owing to contribution of internal microstructures and interfacial roughness. VTXRD (1400C to 250C at constant cooling rate) and MDSC studies revealed crystalline morphology development in annealed samples that can be related to the aspect ratio, microstructure, and functional grs of clays. The overall crystallinity development is less effected in laponite based composites.