The interaction mechanism of nucleic acid with small organic molecules plays an important role in the recognition of the structure and function of nucleic acids, which can also reveal the biological function of nucleic acids and the mechanism of some drugs. Research on the interaction between nucleic acid and small organic molecules plays an important part in simulating the life process and exploring the essence of life. In the present article, detailed description of the fluorescence spectroscopy research methods used in this field is presented. The fluorescence quenching types of the interaction between nucleic acid and small organic molecules(including dyes and drugs)are discussed. There are many factors influencing the fluorescence quenching type, including the temperature, the rate constant of bimolecular quenching process, the fluorescence lifetime, changes of the absorption spectra and so on. So according to different affecting factors, the fluorescence quenching type can be determined based on corresponding theories. Many different kinds of calculation methods are also summarized, including the calculations of the binding constant, the distance between fluorescence donor and receptor, the interaction force type and the binding mode of nucleic acid with small organic molecules. Furthermore, the formation constant of nucleic acid with small organic molecules is studied with different binding numbers. These conclusions have guiding significance for studying the interaction between nucleic acid and small organic molecules. These results can also provide guidance for the development of new nucleic acid probe, and the design of new drug molecules, of which nucleic acid is the important target.