The binding ability andinclusion complexation behavior of natural α-, β-, γ-cyclodextrins (1–3) and two mono[6-oligo(ethylenediamino)-6-deoxy]-β-cyclodextrins(4, 5) with fourChinese traditional medicines, that is, α-asarone (AS), ferulic acid (FA), magnolol (MA) and honokiol (HO), have been investigated in aqueous phosphate buffer solutions(pH = 7.20). The spectral titrations have been performed at 25 °C by using fluorescence spectroscopy to calculate the complex stability constants (KS) and Gibbs free energy changes (Δ G°) for the stoichiometric 1 : 1 inclusion complexation of hosts1–5 with guest medicines. The results obtained indicate that the different guest medicines fit in with hydrophobic cavities of different sizes and the appended substitutes of hosts 4 and 5 change the hydrophobic microenvironment of β-cylcodextrin 2, influencing the original binding ability and molecular selectivity of host 2 consequently. The binding ability and inclusion complexation behavior of these hosts 1–5 are discussed according to the size/shape fit concept and hydrogen bonding interaction between host cyclodextrins and guest medicine molecules.