Abstract: Nucleic acid, one of the most important biological macromolecules in cells, plays a crucial role in the carrying and transmission of genetic information and participates in the regulation of cell fate. Nitrogen mustard was the first anti-tumor drug approved by the U.S. Food and Drug Administration. This type of nucleic acid alkylating agent and the subsequent development of many types of molecules acting directly on nucleic acids became hot topics in drug research and development in the early years. However, due to problems such as selectivity and toxicity, the development of nucleic acid-targeting drug molecules has been quite slow over a long period of time. With the further revelation of the structures, functions and mechanisms of action of nucleic acids in recent years, innovative drug research based on new nucleic acid targets and drug design strategies has regained our attention. This review summarizes recent advancements in this field, encompassing approved molecules and those under clinical trials, so as to provide insights for the development of small molecule drugs targeting nucleic acids.