β-Cyclodextrin (1 -CD) and 2 -cyclodextrin (2 -CD) (hosts) formed inclusion complexes with 4,41-bipyridinium dication derivatives with long chains (guests), in which the substituents on the bipyridinium nitrogen atoms are 1,3-bis(chloromethylphenethyl)-1,1,3,3-tetramethyldisiloxane. The number of 2 -CD molecules threaded onto the polymer chain increases with the length of the guest chain. In contrast, the number of β-CD molecules threaded onto the polymer is approximately 4 corresponding to each molecular chain, due to the repulsive interaction between β-CD and the quaternary bipyridinium units. The complexes were isolated in high yield and characterized by 1H NMR, 13C NMR, X-ray diffraction, thermal and scanning electron micrographs studies. As proven by X-ray analysis, the synthesized polyrotaxanes are crystalline materials with crystalline patterns significantly different from that of native cyclic oligosaccharide. The thermal stabilities of polyrotaxanes are higher than that of the physical mixture between cyclodextrin and the alternating copolymer, denoting the formation of the inclusion complexes. Scanning electron micrographs of polyrotaxanes reveal cubic and linear shapes without a well formed shape. Shape regularity and geometrical regularities in the agglomerating forms can be observed.