Herein, a mono-lacunary Keggin-type polyoxometalate (POM), [SiW11O39]8-, grafted with an azobenzene group through Sn ion bridging was prepared, and the formed organic-inorganic hybrid cluster was characterized via elemental analysis, NMR, TGA, and IR techniques. A vesicular structure of the hybrid cluster assembly in aqueous media was observed in the TEM image, and it dissociated in the presence of α-/β-, γ-cyclodextrins (α-/β-, γ-CDs); this dissociation was driven by the host-guest interactions. The monodispersed inclusion complex further reassembled into smaller micelles under irradiation with 365 nm light, and this transformation was reversibly controlled by alternating the irradiation with 450 nm light. Moreover, in the case of the POM-Azo/β-CD system, reassembly from the monodispersed state to the vesicular state was achieved by the addition of a competitive guest molecule. Thus, the reversible host-guest interactions combining reversible photoisomerization of the azobenzene group provided multiple ways to modulate the assembly and disassembly of the POM hybrid as well as the changes between different assemblies. The present study inspires the potential use of these kind of hybrid POMs in enhanced catalytic reactions and recycling.