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Two [M3L3]6 +-type organo-palladium(II) macrocyclic host molecules, {[(phen)Pd]3(4,7-phen)3}(NO3)6, 1·6NO3−; {[(dtod-phen)Pd]3(4,7-phen)3}(NO3)6, 2·6NO3−, (where M = (4,7-phen)Pd, (dtod-phen)Pd; 4,7-phen = 4,7-phenanthroline (L), phen = 1,10-phenanthroline, dtod-phen = 5,6-di(1′,4′,7′,10′-tetraoxododecanoxy)-1,10-phenanthroline), have been synthesized by metal-directed self-assembly in aqueous solution. These basket-shaped hosts bearing syn, syn, syn orientations and their anion complexes, have been fully characterized by 1H NMR, cold-spray ionization mass spectrometry (CSI-MS) and in the case of basket-shaped host 1*PF6− by X-ray single-crystal diffraction analysis. On the basis of anion binding structure within the cavity of 1, the molecule basket 2 possessing a hydrophobic inner cavity expanded with hydrophilic polyethyleneglycol chains was successfully designed for encapsulating one giant anion [(C2B9H11)2Co]− in water and the host–guest interaction was studied by 1H NMR titration and CSI-MS.