Near-infrared (NIR) fluorescent dyes based on small organic molecules are characterized with low cytotoxicity, good biocompatibility and minimum interference from auto-fluorescence background, which are widely used in tumor diagnosis. Intensive research on molecular properties and photothermal properties of fluorescent dyes have been explored for non-invasive photothermal treatment of cancer. In this review, we focus on the development of imaging-induced photothermal therapy of small molecules and classification according to the structures of organic molecules including cyanines, phthalocyanines, rhodamine analogues and BODIPYs.