We designed and synthesized six polyrotaxanes (PRXs) consisting of lower and higher filling ratios of half-methylated α-cyclodextrin (MeCyD) and the same length of poly (ethylene glycol). The PRXs were used as a crosslink unit to prepare polyurethanes (PU-PRXs) by [NCO]/[OH] ratios (NCO indexes) of 1.0 and 1.5. Since the PU-PRXs left their gel fractions in DMSO, the existence of the crosslinks between PRXs was revealed. The hydrogen bonding formation was affected by the filling ratio of MeCyD. The glass transition temperatures of PU-PRXs depended on the NCO indexes whereas the temperatures of the reorganized crystallization and melting of PU-PRXs were influenced by the filling ratios of MeCyD and lengths of PEG in the PRXs. The tan δ curves indicated that some types of relaxation presented in PU-PRXs with the higher filling ratios of MeCyD. One possibility is the sliding of MeCyDs. The elongations of PU-PRXs with the lower filling ratios of MeCyD were higher than those with the higher filling ratios, implying the sliding effect of PRXs. The best tensile strength and elongation were observed in PU-PRXs with the NCO index of 1.0. The increase in the number of crosslinks seems to result in the improvement of the mechanical properties.