In order to investigate the effects of substituent and tether length in molecular recognition, three novel indolylcontained β-cyclodextrin derivatives were synthesized by the condensation of indol-3-ylbutyric acid with the corresponding oligo(aminoethylamino)-β-cyclodextrin in the presence of DCC. Their molecular recognition behavior with some representative dye guests, i.e. Acridine Red, Rhodamine B, Neutral Red, Brilliant Green and Methyl Orange, was studied by using absorption, fluorescence and circular dichroism spectrometry. From the results of induced circular dichroism spectra and two-dimensional NMR spectroscopy, it was found that the initial conformations of these compounds are dramatically different in aqueous buffers of pH 2.0 and 7.2, which intrinsically determine the molecular binding ability of the host. It was also revealed that both the guest structure and the host tether length were responsible for the inclusion complexation stability. Therefore, on the one hand the hydrophobicity and substituent effect of the guest simultaneously determine the stability of host–guest complex through hydrophobic, van der Waals, and electrostatic interactions. On the other hand, the size/shape-matching relationship and induced-fit concept working between host and guest also play crucial roles in the selective molecular binding process of cyclodextrin hosts.