A preferred geometry of a planar shape-persistent dimeric macrocycle with diacetylene-linked alternating hexylbenzene and perfluorobenzene rings is revealed by resolving its three-dimensional spatial energy profile using density functional theory calculations. The resulting dimer exhibits a face-to-face geometry with about 51.5 degrees rotational off-set around the principal axis and an intermolecular distance of about 3.91 angstrom. The calculated intermolecular interaction energy and the H-1 NMR chemical shifts of the exo- and endo-annular protons of the predicted dimer agree very well with the recent experimental data. More importantly, the current study resolves the ambiguity observed in the experiment pertaining to how the dimer would form, and provides insight for predicting the geometry of similar dimeric macrocycles or other pi-pi interacting systems.