As a promising luminescent nanomaterial, carbon dots (CDs) have received tremendous attention for their great potential in biomedical applications, owing to their distinctive merits of ease in preparation, superior optical properties, good biocompatibility, and adjustable modification in structure and functionalities. However, most of the reported CDs exhibit insufficient excitation and emission in red/near-infrared (R/NIR) regions, which significantly limits their practical applications in biomedical assays and therapy. In the latest years, extensive studies have been performed to produce CDs with intensified R/NIR excitation and emission by designed reactions and precise separations. This review article summarizes state-of-the-art progress towards design and manufacture of CDs with long-wavelength or multicolor emissions, involving their synthetic routes, precursors, and luminescence mechanisms. Meanwhile, the applicable availability of CDs in bioimaging, sensing, drug delivery/release, and photothermal/photodynamic therapy, is systematically overlooked. The current challenges concerning feasible controls over optical properties of CDs and their new opportunities in biomedical fields are discussed.