Thermoreversible gelation and microphase formation of aqueous solutions of a methylated polyrotaxane (MePR) were investigated by means of differential scanning microcalorimetry, rheometry, and X-ray diffractometry (XRD). The aqueous solutions of MePR show a lower critical solution temperature (LCST) and form an elastic gel with increasing temperature. The sol-gel transition of the MePR solutions was induced by formation and deformation of aggregates of methylated alpha-cyclodextrins (alpha-CDs) of polyrotaxane due to hydrophobic dehydration and hydration, respectively. The XRD investigation revealed localization and highly ordered arrangement of methylated alpha-CDs along the PEG chain in the gel. The arrangement of CDs was also reflected by the changes in elasticity and long relaxation behavior of the solution around the sol-gel transition. The quasiequilibrium shear modulus of MePR solutions showed the critical phenomena against temperature. The scaling exponents measured at two different concentrations were almost equal to the values predicted by a gel percolation theory. Therefore, the heat-induced gelation of aqueous MePR solutions is well explained by a model in which clusters assembled with methylated alpha-CDs are gradually connected to the network as the temperature increases.