The multiwalled carbon nanotubes (MWCNTs), Closite 30B nanoplates (CBNPs), and halloysite nanotubes (HNTs) reinforced thermoplastic polyurethane (TPU) nanocomposites were prepared via melt compounding method and evaluated with several techniques including microscopy, spectroscopy, thermal, and rheological analyses. Degree of microphase separation and nucleation efficiency of nanocomposites were calculated. Results showed that at 0.1 wt% nanofiller content, the nanocomposites possess the fastest microphase separation kinetics and the highest degree of microphase separation. Avrami equation was used to analyze the crystallization behavior of samples. Based on the rheological and microscopy analyses, existence of microphase separation above the percolation threshold was observed for annealed samples. Finally, competition between reagglomeration of nanofillers and formation of microphase separated domains above the percolation threshold at various nanofiller contents, shear rates and temperatures was discussed. POLYM. COMPOS., 40:E422–E430, 2019. © 2018 Society of Plastics Engineers