Three naphthalene-modified cyclodextrins (CDs) 3–5 were synthesized as supramolecular chiral photosensitizing hosts for enantiodifferentiating photoisomerization of (Z,Z)-1,3-cyclooctadiene (1ZZ) to its E,Z-isomer (1EZ). In aqueous methanolic solutions, β-CD-based sensitizer 4 binds 1ZZ in its chiral cavity much more strongly than α- and γ-CD homologues 3 and 5. Accelerated, often static, fluorescence quenching of these naphthalene-modified CDs was observed upon inclusion of 1ZZ. The photoisomerization of 1ZZ mediated by 3–5 yielded enantiomeric 1EZ in modest yields. The enantiomeric excesses (ee’s) obtained with α- and β-CD-based sensitizers 3 and 4, both of which have relatively small cavities, are less sensitive to temperature, demonstrating the low-entropy nature of the α- and β-CD complexes. In contrast, increasing reaction temperature significantly diminished the product’s ee and even caused a switching of enantioselectivity upon photoisomerization sensitized by γ-CD-based 5, revealing that the entropy factor plays a crucial role in the wide cavity of γ-CD.