Two functionalized polyoxovanadate-based metal-organic polyhedra with heterocube formations are synthesized under solvothermal conditions. The structures of VMOP-18 and VMOP-19 display similar cuboctahedral geometries when the polyoxovanadate {V6O6(OCH3)9X(COO)3}n- (X = VO4, n = 1; SO4, n = 2) building units and organic ligands are considered as triangular faces of the polyhedra. Each cuboctahedron was surrounded by eight neighbouring cuboctahedra via strong C-Hπ interactions, leading to a 3D open supramolecular structure. Furthermore, the absorption ability toward the ionic dyes of VMOP-18 was investigated. Only cationic dyes can be absorbed into the cavity of VMOP-18, which indicates that the cationic dye absorption process is an ion-exchange process.