We previously reported that the structure of the linker moiety controlled intramolecular and bimolecular aggregation of [3+3]cycloalkyne oligomers, which are cyclic acetylene derivatives containing helicenes. Here, novel [3+3]cycloalkyne dimers linked by the azo group are synthesized, and aggregation behaviors are studied, which turned out to be considerably different. The trans- and cis-azo compounds were synthesized by the oxidative coupling of a [3+3]cycloalkyne amine derivative, and the stereochemistry was determined by UV-vis spectroscopy. 1H NMR, CD, gel permeation chromatography analysis, and vapor pressure osmometry in chloroform revealed that the trans-isomer forms a strong and selective bimolecular aggregate. The cis-isomer forms a trimolecular aggregate at a concentration below 1 mM and a polymeric aggregate at above 1 mM. Unlike known diaryl azo compounds, these azo isomers do not interconvert when subjected to heating or irradiation. In contrast, a model compound lacking the cyclic helicene structure isomerizes readily.