Finally, we look forward to the development direction of small molecule dyes and propose for novel super-resolution fluorescent dyes/probes to achieve high membrane permeability, excellent precision positioning ability, high brightness and stability, and low phototoxicity of dye molecules without increasing the size of dye molecules as much as possible. This paper summarized the structural design characteristics of organic small molecule dyes selected for different techniques with respect to the requirements of different super-resolution imaging techniques for dye performance. It provides ideas for the development of new dyes suitable for super-resolution imaging.