Thioxanthene-hemicyanine is a fluorescent dye in which a nitrogen heterocyclic cation moiety and a terminal amino, hydroxyl or alkoxy amino group are linked by π-conjugated bridge. Thioxanthene-hemicyanine has outstanding photophysical properties and great biocompatibility, and its unique near-infrared emission and photosensitive features enable it to play a crucial role in the study of fluorescence detection and tumor therapy. This article reviews the research and application of thioxanthene-hemicyanine-based fluorescent probes and photosensitive molecules in the recognition of various biomarkers and phototherapy of diseases, respectively.