Cysteine (Cys) is integral to both industrial applications and biological processes. In this study, a novel colorimetric fluorescent sensor APA, defined by its intramolecular charge transfer (ICT) properties, was optimized to effectively discriminate Cys from other structurally similar compounds such as homocysteine (Hcy) and glutathione (GSH). We present the aurone-incorporated fluorescent sensor APA, which features a 4-dimethylaminocinnamaldehyde group conjugated to the aurone scaffold and facilitates selective detection of Cys with a limit of detection (LOD) of 25.7 nM. Compared to previous studies, sensor APA exhibits near-infrared properties, a reduced reaction time of just 2 min, and a significant Stokes shift of 190 nm. Notably, APA has been successfully employed for visual imaging of Cys in test strips and quantitative detection in various food samples in real-time (including garlic, carrot, tomato, onion, green pepper, cauliflower, daikon, lotus root, apple, pear, milk powder, bread, and biscuits). Furthermore, APA has proven effective for colorimetric imaging of both endogenous and exogenous Cys in A549 cells as well as zebrafish and mice models demonstrating its practical biological applications. Overall, our findings highlight the potential of APA as one of the most promising designs for sensing Cys within the food industry and biological systems. Additionally, APA-OH serves as an ideal fluorophore for constructing fluorescence sensors aimed at bioimaging.