Atomic-scale and close-to-atomic scale manufacturing, a frontier hot issue in international academic research, is a cutting-edge manufacturing technique in which atoms are directly used as the manipulation object and atomic-scale structures with specific functions are established to meet the requirements for mass productions. This review focuses on precise atomic-scale manufacturing technology of nucleic acid materials. Firstly, the basic structures and functions of nucleic acid materials are introduced, and the basic principles of the interaction between DNA and metal atoms are discussed. Then the development process and breakthrough progress of nucleic acid materials-mediated precise atomic-scale manufacturing are introduced from the aspects of natural nucleic acid materials, artificial base “molecular elements”, and nucleic acid nanostructures. Finally, the challenges and opportunities in this field are systematically summarized and some suggestions for future development are given.