A rotaxane containing an alpha-CD macrocycle, an azobenzene unit and two different fluorescent naphthalimide units as stoppers has been synthesized. The rotaxane can serve as a photodriven and thermal-driven molecular shuttle. The change of the temperature can make the CD macrocycle shuttle back and forth between the azobenzene and biphenyl stations, and the cis-trans photoisomerization of the azobenzene unit resulted in also the motion of the CD macrocycle on themolecular thread. The absorption and fluorescence spectra of the rotaxane in the different states were studied. The regulation and full reversibility of the fluorescence changes make the molecular shuttle serve as a molecular storage medium or switch with all clean inputs and outputs.