A new approach to the development of functional biomaterials is to obtain a controllable nanostructure through supramolecular self-assembly. Although much effort has been devoted to supramolecular structures with different morphologies and properties, fluorescent macrocycle-based carbon material assembly into three-dimensional vesicle morphologies remains a challenge. Herein, the supramolecular properties of cycloparaphenylene (CPP) in a mixed solution are characterized and controlled successfully through the regulation of different concentrations and solvent ratios. The self-assembled CPP molecules form a three-dimensional hollow structure in different solutions. The assembled vesicle structure endows CPPs with cell biology application and it is found that CPPs could be internalized by cells via an energy- or temperature-independent mechanism. Even in the presence of different inhibitors, cellular uptake of [10]CPP could not be affected. These supramolecular and biological findings of CPPs extend the current understanding of cycloparaphenylene chemistry and will open up new and more attractive applications in nanotechnology, biology and materials science.