Controlling the geometric structures of metal clusters through structural isomerization allows for tuning of their electronic state. In this study, we successfully synthesized butterfly-motif [PdAu8(PPh3)8]2+ (PdAu8-B, B means butterfly-motif) and [PtAu8(PPh3)8]2+ (PtAu8-B) by the structural isomerization from crown-motif [PdAu8(PPh3)8]2+ (PdAu8-C, C means crown-motif) and [PtAu8(PPh3)8]2+ (PtAu8-C), induced by association with anionic polyoxometalate, [Mo6O19]2– (Mo6) respectively, whereas their structural isomerization was suppressed by the use of [NO3]– and [PMo12O40]3– as counter anions. DR-UV-vis-NIR and XAFS analyses and density functional theory calculations revealed that the synthesized [PdAu8(PPh3)8][Mo6O19] (PdAu8-Mo6) and [PtAu8(PPh3)8][Mo6O19] (PtAu8-Mo6) had PdAu8-B and PtAu8-B respectively because PdAu8-Mo6 and PtAu8-Mo6 had bands in optical absorption at the longer wavelength region and different structural parameters characteristic of the butterfly-motif structure obtained by XAFS analysis. Single-crystal and powder X-ray diffraction analyses revealed that PdAu8-B and PtAu8-B were surrounded by six Mo6 with rock salt-type packing, which stabilizes the semi-stable butterfly-motif structure to overcome high activation energy for structural isomerization.