A pair of cyclophane-encapsulated [Cu3(μ3-E)]3+ complexes (E = S and Se) were characterized by resonant X-ray diffraction anomalous fine structure (DAFS), revealing unexpected polarization among the three Cu sites attributed to long-range effects of π-stacking interactions with cocrystallized benzene molecules. The resonant K-edge energies of individual Cu sites within the cluster molecules were found to vary as a function of distance from the cocrystallized benzene. This pattern was interpreted in the context of T-shaped, edge-to-face π-stacking with the assistance of theoretical charge density difference calculations.