Abstract: Scanning transmission electron microscopy (STEM), a necessary tool for the microstructure of materials and microarea analysis, combines the advantages of transmission electron microscopy (TEM) and scanning electron microscopy (SEM), and has the advantages of high-resolution imaging, strong atomic contrast sensitivity, and easy-to-understand visual images. Traditional Chinese medicine research has a long history. Microscopic technology has always been one of the important means to study the micro-characteristics and mechanism of medicinal materials, and is irreplaceable to the other technologies. The principles, methods and technical characteristics of STEM, as well as its application in the microstructure and nanoparticles of traditional Chinese medicine has been reviewed, in order to provide reference for the further expansion of the research on the micro-characteristics of traditional Chinese medicine.