Recent studies have theoretically and experimentally demonstrated that antiaromatic molecules with 4n π electrons exhibit stacked aromaticity according to π-π stacking when arranged in a face-to-face manner. However, the mechanism of its occurrence has not been clearly studied. In this study, we investigated the mechanism of stacked aromaticity using cyclobutadiene. When the antiaromatic molecules are stacked in a face-to-face manner, the orbital interactions between the degenerate singly occupied molecular orbitals (SOMOs) of the monomer unit cause a larger energy gap between the degenerate highest-occupied molecular orbitals (HOMOs) and the lowest-unoccupied molecular orbitals (LUMOs) of the dimer. However, the antiaromatic molecules are more stable in less symmetric conformations, mainly because of pseudo-Jahn-Teller distortions. In the case of cyclobutadiene, the two SOMOs of the monomer unit split into HOMO and LUMO because of the bond alternation. When the molecules are stacked in a face-to-face manner, the HOMO-LUMO gap of the dimer is smaller than that of the monomer due to the interactions between the HOMOs and LUMOs of the two monomer units. When the monomer units are within a specific distance of each other, the HOMO and LUMO of the dimer, which correspond to antibonding and bonding between the units, respectively, are interchanged. This alternation of molecular orbitals may result in an increase in the bond strength between the monomer units, exhibiting stacked aromaticity. We demonstrated that it is possible to control the distance exhibited by stacked aromaticity by engineering the HOMO-LUMO gap of the monomer units.