Photodynamic therapy (PDT) has shown promise as an effective treatment modality for cancer and other localized diseases due to its noninvasive properties and spatiotemporal selectivity. Near-infrared (NIR) fluorescent dyes based on organic small molecules are characterized with low cytotoxicity, good biocompatibility and excellent phototoxicity, which are widely used in PDT. In this review, we attempt to summarize the development of imaging-induced PDT based on organic small molecules and classify it according to the structures of dyes including cyanines, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) analogues, phthalocyanine and other agents such as rhodamine analogues.