6-Deoxy-6-mercapto-β-cyclodextrin is widely used in the pharmaceutical industry for drug delivery systems due to its ability to form inclusion complexes with various drugs, enhancing their solubility and stability. It is also employed in the development of biosensors and nanomaterials, where its thiol group facilitates the attachment of functional molecules or nanoparticles.

Additionally, this compound plays a significant role in environmental applications, such as the removal of heavy metals from wastewater, leveraging its strong binding affinity with metal ions. In analytical chemistry, it is utilized for chiral separation, improving the resolution of enantiomers in chromatographic techniques. Its unique properties make it a valuable tool in both research and industrial applications.