Three polarized aromatic guest molecules (pyrene-4,5-dione, 1) form a triple-layered stack in the box-shaped cavity of an organic pillared coordination cage in water. The cavity size strictly limits the number of stacked planar guests but does not restrict guest orientation, and thus enables the study of discrete stacks of polarized guests and their preferred conformations. Crystallographic study shows that the guest molecules in the cavity are rotated 120 degrees with respect to each other, cancelling the net dipole moment rather than the local dipole moment. The unique conformation of a discrete, triple stack of 1 sharply contrasts to the standard head-to-tail conformation in infinite stacks of 1.