Traditional Chinese Medicine (TCM), which has been used for thousands of years to treat diseases, provides unique theoretical and practical methodologies for disease control. With the increasing accumulation of TCM data, it is imperative to study and analyze these resources with modern technologies and to elucidate the molecular mechanisms of TCM therapy. However, the philosophy, framework and technique of TCM are quite different from those of Western medicine, which causes complications when attempting to design modern drug treatments based on TCM. To meet this challenge, some basic chemoinformatics techniques, including molecular similarity searching, virtual screening and inverse docking, have been utilized in an attempt to gain a deeper understanding of TCM and to accelerate the TCM-based drug discovery. Recent progress on the use of chemoinformatics in TCM research will be discussed and an example of the preliminary application of chemoinformatics methods in anticancer drug design will be provided.