Only a limited number of multinucleating ligands can stably maintain multinuclear metal structures in aqueous solutions. In this study, a water-soluble dinucleating ligand, 2,6-bis{[N-(carboxylatomethyl)-N-methyl-amino]methyl}-4-methylphenolate ((sym-cmp)3−), was prepared and its copper(II) complexes were structurally characterized. Using the single-crystal X-ray diffraction method, their dimer-of-dimers type defect cubane tetranuclear copper(II) structures were characterized for [Cu4(sym-cmp)2Cl2(H2O)2] and [Cu4(sym-cmp)2(CH3O)2(CH3OH)2]. In the complexes, each copper(II) ion has a five-coordinate square-pyramidal coordination geometry. The coordination bond character was confirmed by the density functional theory (DFT) calculation on the basis of the crystal structure, whereby we found the bonding and anti-bonding molecular orbitals. From the cryomagnetic measurement and the magnetic analysis, overall antiferromagnetic interaction was observed, and this magnetic behavior is also explained by the DFT result. Judging from the molar conductance and the electronic spectra, the bridging chlorido ligand dissociates in water, but the dinuclear copper(II) structure was found to be maintained in an aqueous solution. In conclusion, the tetranuclear copper(II) structures were crystallographically characterized, and the dinuclear copper(II) structures were found to be stabilized even in an aqueous solution.