The thermal properties and morphological development of isothermally crystallized isotactic polypropylene (iPP) blended with nanostructured polyhedral oligomeric silsesquioxane (POSS) molecules at very small loading of POSS were studied with differential scanning calorimeter (DSC), thermal gravimetric analysis, dynamic mechanical analysis, polarized optical microscopy (POM), and wide-angle X-ray diffraction (WAXD). The result of DSC indicated that the crystallization rate of iPP increases with the increase in POSS contents during crystallization; moreover, the melting temperature of iPP/POSS nanocomposites slightly decreases, while the heat of fusion increases with the addition of POSS molecules at melting and remelting traces. The storage modulus and thermal stability, respectively, remarkably decrease, while the glass transition temperature of isothermally crystallized iPP/POSS nanocomposites increases slightly with the increase in POSS contents. The morphologies results of WAXD and POM show that the POSS molecules form about 35 nm sized nanocrystals and aggregate to form thread-like and network structure morphologies, respectively, in the molten state even when the POSS content is very small. These results, therefore, suggest that the interaction force between the POSS molecules should be larger than the force between POSS molecules and iPP matrix; however, those interactions depend on the chain length of functionalized substituents on the POSS cage. Therefore, the POSS molecules aggregate forming nanocrystals and act as an effective nucleating agent for iPP and influence the thermal properties of iPP/ POSS nanocomposites due to the shorter chain length of functionalized substituents, methyl, on the POSS cage.