Metal ions possess abundant electrons and unoccupied orbitals, as well as large atomic radii, whose doping into carbon dots (CDs) is a facile strategy to endow CDs with additional physicochemical characteristics. After being doped with metal ions, CDs reveal obvious changes in their optical, electronic, and magnetic properties by adjustments to their electron density distribution and the energy gaps, leading them to be promising and competitive candidates as labeling probes, imaging agents, catalysts, nanodrugs, and so on. In this review, we summarize the fabrication methods of metal‐ion‐doped CDs (M‐CDs), and highlight their biological applications including biosensing, bioimaging, tumor therapy, and anti‐microbial treatment. Finally, the challenging future perspectives of M‐CDs are analyzed. We hope this review will provide inspiration for further development of M‐CDs in various biological aspects, and help readers who are interested in M‐CDs and their biological applications.