Apparent formation constants and thermodynamic parameters of inclusion complexation of 3-hydroxynaphthalene2-carboxylic acid (3H2NA) and its analogues with cyclodextrins in aqueous solutions were determined by the steady-state fluorescence Benesi–Hildbrand method at various pH values. The pH dependence of formation constants and thermodynamic parameters for 3H2NA complexing with β-cyclodextrin (β-CD) is different from that with heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (TMβ-CD). Hydrogen bonding between 3H2NA (neutral or ionic form) and β-CD or proton-acceptors such as hydrogen ion and alkoxide ion (formed by dissociation of the secondary hydroxy group of β-CD) and its effect on the stability of the cyclodextrin complex are studied systematically and discussed in detail. It can be concluded that hydrogen bonding plays an important role in the formation of the inclusion complexes. In addition, enthalpy and entropy changes both contribute to inclusion complexation when the guest exists mainly as its molecular form. However, when the guests fully ionize, inclusion complexation is solely driven by enthalpy. The effect of host cavity size, guest diameter and position of substituents on the stability of the complexes is also observed. Linear compensatory ΔH° vs.TΔS° plots give slopes (α = 1.20 ± 0.10 and 1.21 ± 0.01) and intercepts (TΔS°₀ = 19.1 ± 2.5 and 20.7 ± 0.3 kJ mol⁻¹) for native CDs and modified CDs, respectively. On the basis of the enthalpy–entropy compensation effect, the big slopes of the ΔH° vs.TΔS° plots indicate that the structure of native and modified CDs in aqueous solution is flexible, despite the rigid skeleton of native CDs in the solid state, while the large intercepts TΔS°₀ for native and modified CDs indicate extensive desolvation of both the host and guest on host–guest complexation. These two different CDs may be considered as one kind on the basis of enthalpy–entropy compensation effect. The general validity of the enthalpy–entropy effect is supported by the present results.