Compatibility mechanism study of Chinese herbal compound (CHC) has been one of key contents in Chinese medical research, but the present research methods are not suitable for its own features due to its complexity, which has restricted the process of modernization and intemationalization of Chinese medicine. In this paper, we addressed that the compatibility is closely correlated to their in vivo metabolic processes. The preparation of active small molecules monoclonal antibodies in herbs and testing a variety of effective compositions simultaneously using immunoassay can clarify the in vivo metabolism and mutual interactions of Chinese herbs, which is a new thought of studying the compound compatibility mechanisms.