Cysteine (Cys) plays an important role in many physiological activities of human beings. Various diseases are always accompanied by abnormal levels of Cys. A series of Cys-responsive probes were recently developed. However, most fluorescent probes have many disadvantages and exhibit poor in vivo imaging. Therefore, a near-infrared fluorescence (NIRF)/photoacoustic (PA) dual-mode probe with high selectivity and sensitivity (limit of detection = 10.6 nM) toward Cys was developed in this study. The new Probe I interacted with Cys to activate NIRF/PA signals, detecting Cys in vitro with a large emission wavelength (851 nm) and Stokes shift (191 nm), monitoring the occurrence of liver cancer in vivo. This work not only presented an effective NIRF/PA dual-mode dicyanoisophorone probe for the first time in the imaging of Cys but also provided a comprehensive and accurate tool for detecting different analytes and tumors in deeper tissues, which could be conducive to the early diagnosis of diseases.