Near-infrared dyes have attracted widespread attention due to their intense absorption and emission in the near-infrared region. As an important class of heteroatom-containing BODIPY derivatives, Aza-BODIPY dyes display excellent performances, such as red-shifted spectra, high molar extinction coefficients, and good photostability. In this review, we summarize the latest advances in Aza-BODIPY dyes. The regulation strategies for photophysical properties and their applications in biomedical imaging are highlighted. Furthermore, we discuss the versatile imaging applications of Aza-BODIPY dyes in cancer diagnoses, organ injuries, and surgical navigation. The future challenges and development prospects of Aza-BODIPY dyes in biomedical field are also presented. We aim at providing meaningful inspiration for further development of functional organic dyes with excellent properties. It is believed that this review will illuminate the way for the development of new Aza-BODIPY contrast agents as well as other organic photosensitizer-based contrast agents in future clinical practices.