Sulfur-substituted dicyanomethylene-4H-chromene (DCM) derivatives based on the intramolecular charge transfer (ICT) mechanism were designed as near-infrared (NIR) fluorescent dyes. Using the Knoevenagel condensation method, the S-DCM-OH (835) fluorescence dye was synthesized, which had an emission wavelength exceeding 800 nm and 220 nm of a Stokes shift. Compared to commercial ICG, S-DCM-OH (835) was not only synchronized in emission wavelength but also far superior in Stokes shifts. These advantages made the design of S-DCM-NIR (835) based on this dye potentially valuable for biological applications. Based on this chemical structure, a fluorescent S-DCM-NIR (835) nanoprobe with a mean diameter of 17.69 nm was fabricated as the NIR imaging nanoprobe. Results showed that the nanoprobe maintained the high-specificity identification of cysteine (Cys) via the Michael addition reaction, with the detection limitation of 0.11 μM endogenous Cys. More importantly, in an ischemic stroke mouse model, the S-DCM-NIR (835) nanoprobe could monitor the Cys concentration change at stroke lesion due to the disruption of Cys metabolism under the ischemic stroke condition. Such a S-DCM-NIR (835) nanoprobe could not only differentiate the severity of the ischemic stroke using response time but also quantify the concentration of Cys in real-time in vivo.