Abstract: The aggregation state of matter at different scales is the key factor to determine its properties. Structural Chinese medicine is a new cross field of Chinese medicine to study the composition and structure characteristics, formation mechanism, fate in vivo and functional correlation of clusters and aggregates naturally existing or formed by processing in traditional Chinese medicine (TCM). Compared with the traditional molecular level research of TCM, the research objects of structural Chinese medicine have the characteristics of cross-scale, heterogeneity and multi-effect. It is a re-understanding and re-study of the pharmacodynamic substances and the effective mechanism of TCM from the mesoscopic perspective and spatial dimension. External use has been the characteristic of TCM for thousands of years, but lack of in-depth explanation. Taking the external use of TCM as an example, this paper analyzes the common and individual problems existing in the research of TCM, and puts forward the research path based on the thinking of structural Chinese medicine, in order to provide reference for the related fields.