Molecular Systems Engineering is an emerging field by understanding the fundementals of molecular properties and dynamics in synthetic complex systems, and exploring sophisticated functions for advanced applications in biomedicine, materials and energy. Our laboratory uses the tools of dynamic combinatorial chemistry (DCC), supramolecular chemistry and computer chemistry to fabricate the framework of complex chemical systems, investigates the self-assembly in such systems and uncovers the working principles at molecular level behind them. We have learned that self-assembly can not only direct the formation of beautiful and intriguing structures i.e. catenanes and “Russian-doll”-like supramolecular architectures, but also promote the molecules to make copies of themselves as the living matters in nature. Currently we are trying to extend the board of DCC into the fields of materials science for cancer treatment.