Derivations of mono-substituted polyhedral oligomeric silsesquioxanes (POSS) with long aliphatic chains were synthesized and self-assembled structures were investigated. The effects of the alkyl chain length and branching on the thermal self-assembling behaviors of the POSS derivatives were examined by differential scanning calorimetry (DSC) and polarized optical microscopy (POM). In addition, small- and wide-angle X-ray scattering (SAXS/WAXS) as well as transmission electron microscopy (TEM) were employed to elucidate their self-assembled morphologies. Long-range straight ordered lamellar structures with sharp boundaries could be reliably formed in the bulk samples of alkylated cage silsesquioxanes by thermal annealing. Furthermore, this research demonstrates an approach to precisely control the feature size at the nanometer scale by carefully tuning parameters of alkyl chain length and branching number.