Determining accurate quantitative values for the changes in the thermodynamic functions caused by molecular inclusion in the liquid phase is essential, since the thermodynamic functions constitute basic information required for understanding the mechanisms of molecular recognition and discrimination. In this study, ideal gas phase enthalpies, entropies, and Gibbs free energies of the inclusion of alcohols and diols into cyclodextrin (CyD) cavities were determined on the basis of experimentally measured calorimetry data and hydration thermodynamic functions. Hydration Gibbs energies of guest molecules were predicted using the SM8 model with dispersion-corrected density functionals. To clarify details related to the interaction energies of β-CyD-drug complexes, pair interaction energy decomposition analysis (PIEDA) was carried out. Further, in order to reveal the mechanism involved in the inclusion phenomenon in these complexes, binding free energies were determined using a molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) analysis. By examining three-body interactions with the molecular orbital method, the differences between homochiral interactions and heterochiral interactions were found to correspond to the excess enthalpies of mixing of the enantiomers. The relationship between molecular interactions and changes in thermodynamic quantities examined by precise microcalorimetry has been reinforced using computational chemistry methods.