To further reveal the factors governing the supramolecular assembly of beta-cyclodextrin (beta-CD) inclusion complexes, two aggregates (1 and 2) were prepared from the inclusion complexes of beta-CD with 4-hydroxyazobenzene and 4-aminoazobenzene, respectively, and their binding behavior were investigated by means of X-ray analysis, UV-vis, NMR, and circular dichroism spectra in both solution and the solid state. The obtained results indicated that the beta-CD/4-hydroxyazobenzene complex 1 could form head-to-head dimers (triclinic system, space group P1) in the solid state, which were further self-assembled to a linear supramolecular architecture by the intra- and interdimer hydrogen bond interactions as well as the intradimer pi-pi interactions. However, when the included guest 4-hydroxyazobenzene was switched to a 4-aminoazobenzene, the resultant beta-CD/4-aminoazobenzene complex 2 (monoclinic system, space group P2(1)) could be self-assembled to a wave-type supramolecular aggregate under similar conditions. Furthermore, the combination of crystallographic and spectral investigations jointly revealed the inclusion complexation geometry of beta-CD with 4-hydroxyazobenzene and 4-aminoazobenzene in both solution and the solid state, which demonstrated that the disparity of substituents in the azobenzenes played an important role in the inclusion complexation and molecular assembly, affecting not only the structural features of aggregates but also the binding abilities of azobenzenes with beta-CD.