Presented here are binuclear Nb-2, tetranuclear Ti2Nb2, and dodecanuclear Nb-12 complexes decorated by embonic acid ligands. These structures feature a unique Ti-O-Nb or Nb-O-Nb subunit. Besides, the unprecedented dodecanuclear Nb-12 cluster further displays a porous three-dimensional packing framework and stability in water, affording an interesting selective uptake for methylene blue molecules over rhodamine B.