A disodium tetrakis(phthalimide) palladium(II) complex, [Na2Pd(phthal)4] (1), was synthesized by reaction of four phthalimide molecules with Pd(OAc)2 in the presence of Et3N. The above and below axial sites of the Pd coordination plane formed the spaces suitable for capturing Na+ ions, which were coordinated with the four imidato oxygen atoms. The complex 1 was linked through the Na+ ions bridged by the water molecules, building an infinite chain structure along the crystallographic a axis. The four phthalimidato moieties contacted in the four orthogonal directions together through their π-π stacking interaction. Such a self-assembly of molecule 1 constructed nanopores with a pore size of ca. 3 × 4 Å in the crystals.