Fluorescent metal nanoclusters (MNCs), composed of a few to hundreds of noble metal atoms, are a type of sub-nanometer scale transitional material between atoms and nanoparticles. The special structure and size endow MNCs with a series of excellent fluorescence properties, such as strong fluorescence, high quantum yield, good anti-photobleaching, and mega-Stokes shift. In addition, MNCs show advantageous properties with respect to good biocompatibility and water solubility. These properties have made MNCs new metal nano-fluorophores (MNFs) that are widely used in biochemical analysis and bioimaging. Among the various scaffolds for the stabilization of MNCs, deoxyribonucleic acid (DNA) is an interesting ligand due to its unique structure and programmable sequences. The properties of DNA-templated MNCs, such as the excitation/emission wavelength, fluorescence intensity, and the sizes of the MNCs, can be controlled by DNA templates with different sequences, lengths or configurations. We call DNA-templated MNCs “DNA-coded MNFs” here. In this review, based on our previous studies on DNA-templated MNCs, we focus on systematically summarizing the preparations, property regulations and applications of DNA-coded MNFs in biosensing and bioimaging. Finally, the current challenges, research emphases and prospects of DNA-coded MNFs are also discussed. We believe that this review will promote the development of this fertile research area in the future.