Herein, we describe how to utilize stacking interactions to achieve selective supramolecular transformation and molecular Borromean rings (BRs). By using a dinuclear naphthalenediimide (NDI)-based Cp*Rh acceptor and linear bipyridyl ligands, organometallic rectangles featuring dynamic behavior have been constructed. Unique discrete aromatic stacking arrays were formed by inducing pyrene units as guest molecules. The topology of the BRs was realized by the use of a strategically chosen ligand which was capable of participating in D-A interactions and hydrogen bonding, as evidenced from single-crystal X-ray analysis and computational studies. These self-assembly processes underline the advantages of dynamic bonding and π-π stacking interactions, and serve to illustrate a new approach to generating structurally and topologically nontrivial supramolecular architectures.