Aryl-perfluoroaryl interaction was used for the crystal engineering of photochromic diarylethene derivatives. A diarylethene derivative having pentafluorophenyl groups, 1,2-bis(2-methyl-5-pentafluorophenyl-3-thienyl)perfluorocyclopentene (1a), formed 1:1 stoichiometric cocrystals with different diarylethenes, 1,2-bis(2-ethyl-5phenyl-3-thienyl)perfluorocyclopentene (2a) and 1,2-bis[2-methyl-5-(l-naphthyl)3-thienyl]perfluorocyclopentene (3a). In the cocrystals 1a* 2a and 1a* 3a, highly selective photocyclization reactions of 2a or 3a were observed. Unique nanostructures in which the colorless and colored molecules were periodically arranged were constructed in the photoirradiated cocrystals.