We developed a highly selective ratiometric near-infrared cyanine-based probe CyAC for cysteine (Cys) over homocysteine (Hcy) and glutathione (GSH). Upon the addition of Cys to the solution of CyAC, remarkable shifts in the spectra of CyAC can be monitored (from 770 nm to 515 nm in absorption spectra and from 780 nm to 570 nm in emission spectra). For the first time, the novel strategy that reversibly modulates the polymethine π-electron system by conjugation and removal of the specific trigger moiety was implemented for the generation of a ratiometric cyanine-based sensor. Hydroxy cyanine CyAE was chosen as the flurophore scaffold because the tautomerism (CyAE and CyAK or CyAD) can cause the reversible change in the π-conjugation system of the dyes with large shifts in the spectra. An acrylate group containing a α, β-unsaturated ketone as a functional trigger moiety was incorporated with CyAK to form the sensor CyAC. This specific response for Cys was based on the differences of the kinetics of intramolecular adduct/cyclizations. Moreover, CyAC was successfully applied for bioimaging Cys in living cancer cells. This paradigm by modulation of the polymethine π-electron system in the cyanine dye provides a promising methodology for the design of ratiometric cyanine-based sensors.