Traditional Chinese Medicine (TCM) formulas, based on the principles of Chinese medicine, have a long history and are widely applied in the treatment of diseases. Compared to single-component drugs, TCM formulas demonstrate superior therapeutic efficacy and fewer side effects owing to their synergistic effects and mechanisms of detoxification and efficacy enhancement. However, various drawbacks, such as the uncertainty of functional targets and molecular mechanisms, poor solubility of components, and low bioavailability, have limited the global promotion and application of TCM formulas. To overcome these limitations, self-assembled aggregate (SA) nanotechnology has emerged as a promising solution. SA nanotechnology significantly enhances the bioavailability and anti-tumor efficacy of TCM by improving its absorption, distribution, and precise targeting capabilities, thereby providing an innovative solution for the modernization and internationalization of TCM. This review delves into the nature and common interactions of SAs based on the latest research developments. The structural characteristics of SAs in TCM formulas, paired-herb decoctions, and single-herb decoctions are analyzed and their self-assembly mechanisms are systematically elucidated. In addition, this article elaborates on the advantages of SAs in cancer treatment, particularly in enhancing the bioavailability and targeting capabilities. Furthermore, this review aims to provide new perspectives for the study of TCM compatibility and its clinical applications, thereby driving the innovative development of nanomaterials in this field. On addressing the technological challenges, SAs are expected to further promote the global application and recognition of TCM in the healthcare sector.