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Abstract: A series of rod‐shaped polyoxometalates (POMs) [Bu4N]7[Mo6O18NC(CH2O)3MnMo6O18(OCH2)3CNMo6O18] and [Bu4N]7[ArNMo6O17NC(CH2O)3MnMo6O18(OCH2)3CNMo6O17NAr] (Ar=2,6‐dimethylphenyl, naphthyl and 1‐methylnaphthyl) were chosen to study the effects of cation–π interaction on macroionic self‐assembly. Diffusion ordered spectroscopy (DOSY) and isothermal titration calorimetry (ITC) techniques show that the binding affinity between the POMs and Zn2+ ions is enhanced significantly after grafting aromatic groups onto the clusters, leading to the effective replacement of tetrabutylammonium counterions (TBAs) upon the addition of ZnCl2. The incorporation of aromatic groups results in the significant contribution of cation–π interaction to the self‐assembly, as confirmed by the opposite trend of assembly size vs. ionic strength when compared with those without aromatic groups. The small difference between two aromatic groups toward the Zn2+ ions is amplified after combining with the clusters, which consequently triggers the self‐recognition behavior between two highly similar macroanions. [ABSTRACT FROM AUTHOR]