A three-dimensional, highly symmetric sphere-like nanocage was synthesized using a terpyridine (tpy)-based, flexible tris-dentate ligand and characterized by single crystal X-ray analysis. To introduce more rigidity, one of the tpy units of the tris-dentate ligand was preblocked by stable <tpy-Ru2+-tpy> connectivity to form the corresponding Ru2+-dimer. The complexation between Ru2+-dimer and Fe2+ demonstrates an unexpected temperature-dependent assembly between two irreversible isomeric 3D nanocages. Investigation of the coordination process and structural configurations of the metal-ligand framework, affected by the introduction of rigidity and in the presence of external stimuli (temperature), is reported.