Two channel-type supramolecular aggregations 1 and 2 were prepared by the inclusion complex of beta-cyclodextrin with 2,2'-dipyridine and 4,4'-dipyridine, respectively, and their binding ability and assembly behavior were investigated comprehensively by X-ray crystallography, (1)H NMR, circular dichroism spectra, and microcalorimetric titration in solution and the solid state. The obtained results revealed that the hydrogen bonds and pi-pi stacking interactions are crucial factors for the formation of the molecular aggregations containing beta-cyclodextrin and dipyridines. The disparity of nitrogen atom position in dipyridines leads not only to the distinct crystal system and space group, i.e., monoclinic system (C2) for 1 and triclinic system (P-1) for 2, but also different binding modes and thermodynamical parameters upon complexation of 2,2'-dipyridine and 4,4'-dipyridine with beta-cyclodextrin in aqueous solution.