A [3]rotaxane molecular shuttle containing two alpha-cyclodextrin (alpha-CD) macrocycles, an azobenzene unit, a stilbene unit, and two different fluorescent naphthalimide units has been investigated. The azobenzene unit and the stilbene unit can be E/Z-photoisomerized separately by light excited at different wavelengths. Irradiation at 380 nm resulted in the photoisomerization of the azobenzene unit, leading to the formation of one stable state of the [3]rotaxane (Z1-NNAS-2CD); irradiation at 313 nm resulted in the photoisomerization of the stilbene unit, leading to the formation of another stable state of the [3]rotaxane (Z2-NNAS-2CD). The reversible conversion of the Z1 and Z2 isomers back to the E isomer by irradiation at 450 nm and 280 nm, respectively, is accompanied by recovery of the absorption and fluorescence spectra of the [3]rotaxane. The E isomer and the two Z isomers have been characterized by 1H NMR spectroscopy and by two-dimensional NMR spectroscopy. The light stimuli can induce shuttling motions of the two alpha-CD macrocycles on the molecular thread; concomitantly, the absorption and fluorescence spectra of the [3]rotaxane change in a regular way. When the alpha-CD macrocycle stays close to the fluorescent moiety, the fluorescence of the moiety become stronger due to the rigidity of the alpha-CD ring. As the photoisomerization processes are fully reversible, the photo-induced shuttling motions of the alpha-CD rings can be repeated, accompanied by dual reversible fluorescence signal outputs. The potential application of such light-induced mechanical motions at the molecular level could provide some insight into the workings of a molecular machine with entirely optical signals, and could provide a cheap, convenient interface for communication between micro- and macroworlds.