Recently, a terbium(III) double-decker phthalocyaninato (Pc) complex has attracted much attention because of its single molecular magnet (SMM) behavior. One of the most important factors for its magnetic property is the molecular structure. Unfortunately, there are only three available X-ray crystallographic structures of TbPc2 complexes in Cambridge Structural Database (CSD). One is a structure of the neutral TbPc2 complex and others are those of anion complexes containing counter ions. Because of the existence of the counter ions, neutral and anion complexes have different packing structures in the crystal. Interestingly, the X-ray structures indicate that two Pc-rings of the anion complexes are concave and distorted, while those of the neutral complex are flat and parallel. There are two possibilities of a reason for the concave Pc-rings, i.e., the Coulomb repulsion between two Pc-rings due to their negative charges (Pc2– and Pc–), and the intermolecular interaction between adjacent TbPc2 complexes or counter ions. In other words, the problem is whether the concave structure is a nature of the single molecule or not. On the other hand, some DFT calculations predicted concave Pc-ring structures even in the neutral complex, suggesting that the concave structure is the nature of the single molecule. However, it is well known that the conventional and hybrid DFT functional sets do not include a sufficient dispersion interaction such as the van der Waals force. In fact, the experimental distances between two Pc-rings in the complexes are about 2.8–2.9Å, which are much shorter than the face-to-face distance between aromatic compounds in molecular crystals due to the coordination to Tb(III) ion. Therefore, the dispersion interaction between two Pc-rings that consist of many π electrons seems to be important for determining the structure of the complexes. Recently, some functional sets have been developed to correct the dispersion interaction. For example, Grimme and co-workers proposed a new DFT functional set with an empirical dispersion interaction correction (DFT-D). In this study, therefore, we optimized the molecular structures of anion and neutral TbPc2 complexes by using the DFT and DFT-D methods. Calculated results indicated that Pc-rings are flat and parallel with each other both in anion and neutral complexes if the dispersion interaction is included. In addition, the optimized structure of the neutral complex with the DFT-D method reproduced the X-ray structure well. The results show that the distorted Pc-ring is not the nature of the TbPc2 complexes themselves. In addition, the HOMO-LUMO gap in the DFT-D structure is shown to be different from that in the DFT structure. This indicates that taking account of dispersion interaction is indispensable for investigating molecular properties of these complexes by DFT calculations.