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,Bmeans butterfly-motif) and [PtAu8(PPh3)8]2+(PtAu8-B) by the structural isomerization from crown-motif [PdAu8(PPh3)8]2+(PdAu8-C,Cmeans 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) hadPdAu8-BandPtAu8-Brespectively becausePdAu8-Mo6andPtAu8-Mo6had 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 thatPdAu8-BandPtAu8-Bwere surrounded by sixMo6with rock salt-type packing, which stabilizes the semi-stable butterfly-motif structure to overcome high activation energy for structural isomerization.