Polyrotaxanes consisting of cyclodextrin rings, polyethylene glycol axes and quantum dot (QD) stoppers were synthesized and characterized. The molecular self-assembly of polyrotaxanes led to spindlelike nano-objects whose shape, size and position were dominated by QD stoppers. Due to their well-defined molecular self-assemblies, carbohydrate backbone, high functionality and several types of functional groups together with the high luminescence yield, synthesized hybrid nanostructures were recognized as promising candidates for biomedical applications. The potential applications of the molecular self-assemblies as drug-delivery systems was investigated by conjugation of doxorubicin (DOX) to their functional groups and then release the drug inside the cancer cells in mouse tissue connective fibroblast adhesive cell line L929. It was found that the molecular self-assemblies quickly transfer through the cell membrane and slowly release the drug into the intracellular environment. MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) and cell cycle assays showed that the molecular self-assemblies degrade back into individual molecules that can be broken down by the cell metabolically, confirming that they can be used as new drug-delivery systems with high treatment efficacy and minimum side effects for future cancer therapy, thus forming a firm foundation for further study and improvement.