Traditional Chinese medicine (TCM) has been widely used and proven effective in long term clinical practice. However, the molecular mechanism of action for many TCMs remains unclear due to the complexity of many ingredients and their interactions with biological receptors. This is one of the major roadblocks in TCM modernization. In order to solve this problem, we have developed TCMAnalyzer, which is a free web-based toolkit allowing a user to (1) identify the potential compounds that are responsible for the bioactivities for a TCM herb through scaffold-activity relation searches using structural search techniques, (2) investigate the molecular mechanism of action for a TCM herb at the systemic level, and (3) explore the potentially targeted bioactive herbs. The toolkit can result in TCM networks that demonstrate the relations among natural product molecules (small molecular ligands), putative protein targets, pathways, and diseases. These networks are graphically depicted to reveal the mechanism of actions for a TCM herb or to identify new molecular scaffolds for new chemotherapies. TCMAnalyzer is freely available at http://www.rcdd.org.cn/tcmanalyzer .