Three polyoxovanadate-based metal–organic cages, [NH2Me2]8{[V6O6(OMe)9(SO4)]4(BPT)4}·(MeOH)11 (HNU-85), [NH2Me2]8{[V6O6(OMe)9(SO4)]4(BPT)4}·(MeOH)8 (HNU-86), [NH2Et2]4{[V6O6(OMe)9(VO4)]4(BPT)4}·(MeOH)8 (HNU-87), were synthesized based on polyoxovanadates and H3BPT (H3BPT = biphenyl-3,4′,5-tricarboxylic acid) ligand under solvothermal conditions. The structure revealed that HNU-85 ∼ HNU-87 display distorted cuboctahedral geometries when the organic ligands and polyoxovanadate-based secondary building units are regarded as triangular faces of the cages. HNU-85 and HNU-86 are two supramolecular isomers based on the cuboctahedral synthons with various packing modes. The two structural divergences can be ascribed due to the addition of template molecules. HNU-85 and HNU-87 have the similar packing modes with different SBUs. Furthermore, we have explored the adsorption capacity of I2 considering the different pore sizes generated during the stacking process of HNU-85 and HNU-86. The results showed that both HNU-85 and HNU-86 had high I2 adsorption capacity with the maximum adsorption capacities being 190 mg/g and 158 mg/g, respectively. The adsorption process was determined to be monolayer adsorption and followed a pseudo-second-order kinetic model.