3-trans-Stilbene amide-α-cyclodextrin (3-trans-Sti-α-CD) formed a double-threaded dimer in aqueous solutions. In contrast, the photoisomerization of the stilbene moiety in 3-Sti-α-CD from trans to cis leads to the structural changes from the double-threaded dimer to nonthreaded supramolecular assemblies in aqueous solutions. The structures of these supramolecular complexes have been found to be controllable by photoirradiation.