A series of 6-(ω-aminoalkylamino)-6-deoxy-γ-cyclodextrins (CDs) 5–8 with varying inter-amino distances were synthesized to control the stereoselectivity of [4+4] photocyclodimerization of 2-anthracenecarboxylate (AC). Complexation behavior of these CD hosts with AC was studied in aqueous solutions by UV-vis and circular dichroism spectral titration. Supramolecular photocyclodimerization of AC mediated by the CDs was performed in water as well as in water–methanol mixture to reveal that aminopropylamino-CD 6 leads to the formation of head-to-head photodimers 3 and 4 in highest yields, while aminobutylamino-CD 7 affords chiral syn-head-to-tail and anti-head-to-head photodimers 2 and 3 in highest enantioselectivities. These results indicate that the inter-amino distance critically control the product's stereo- and enantioselectivities through the electrostatic interactions of two anionic AC guests with the dicationic sidechain attached to the γ-CD rim and can be used as a convenient, yet effective, tool for manipulating the stereochemical outcomes of supramolecular photochirogenesis.