Polyrotaxanes with a low threading ratio of alpha-cyclodextrin (alpha-CD) on a poly(ethylene glycol) chain effectively acted as both the relaxation and reinforcing reagents in Novolac-type epoxy resin. The polyrotaxanes were incorporated into the epoxy resin during the curing process to produce transparent and rigid epoxy resin/polyrotaxane (E/PR) alloys. From dynamic mechanical analysis (DMA) of the E/PR alloys, it was found that the polyrotaxane contributed not only as a stress-relaxation component but also as a reinforcing modifier in the epoxy resin matrix. The morphology and chemical Structures of polyrotaxanes in the epoxy resin matrices were assumed to be in a nanoscale dispersion, forming an interpenetrate network structure with multi crosslinking bonds on threaded alpha-CDs. This assumption was made based on their transparency, differential scanning calorimetry, small-angle X-ray scattering, and DMA analyses. This is the first report on the unique properties of polyrotaxanes added in a rigid matrix.