Supramolecular control of the π-stacked configuration of aqueous phthalocyanine (Zn[Pc(SO(3))(4)]) was achieved, allowing organization of a J-type slipped-cofacial dimer with per-O-methylated α-cyclodextrin (TMe-α-CDx) by the aid of host-guest interactions. Pristine Zn[Pc(SO(3))(4)] forms nonfluorescent face-to-face aggregates in water. The π-stacked configuration was controlled in the slipped-cofacial dimer, which was formed as a shallow inclusion complex with TMe-α-CDx, giving remarkably enhanced fluorescence with a very small Stokes shift. Organization of the J-type slipped-cofacial dimer as a 2:2 Zn[Pc(SO(3))(4)]-TMe-α-CDx complex was achieved through π-stacking of the unencapsulated segment of Zn[Pc(SO(3))(4)] shallowly encapsulated by a small TMe-α-CDx cavity.