Carbon dots (CDs), as a rapidly developing class of luminescent nanomaterials have been widely studied due to exceptional photostability, ultrasmall size, and facile surface functionalization. Especially, near-infrared fluorescence CDs (NIR-CDs) in the window (650–1700 nm) show great promise in the biomedical field such as sensing, bioimaging, phototherapy, and integrated theranostics. Recent advances have focused on controlled synthesis and precise modulation of the photophysical properties of NIR-CDs to expand their biomedical utility. In this review, we systematically summarize strategies for the preparation of NIR-CDs, emphasizing precursor selection, reaction engineering, and post-synthetic modifications that enable red-shifted and stable emissions. We further highlight mechanistic insights into their luminescence, covering contributions from core, surface, and molecular states, as well as approaches for tailoring optical performance through heteroatom doping, surface engineering, self-assembly, and hybridization. The biomedical applications of NIR-CDs in high-sensitivity biosensing, deep-tissue fluorescence and multiphoton imaging, and synergistic photothermal/photodynamic therapy are critically evaluated. Finally, we discuss current challenges, including limited quantum yields in the NIR-II region, unclear metabolic pathways, and synthetic reproducibility, and propose future directions toward clinical translation. This review aims to provide an integrated perspective that bridges fundamental design principles with emerging applications, thereby guiding the development of next-generation functional carbon nanomaterials.
