Efficacy and safety are not only the solid foundation of traditional Chinese medicine (TCM)'s heritage and development, but also the fundamental premise of TCM serving the health of people in the world. Therefore, integrated analyzing the material basis, action mechanism and toxicity-efficacy relationship of Chinese materia medica's efficacy and safety through multidisciplinary, in addition to revealing the scientific connotation “There is no death, drugs should be removed after recover.”, are the key problems to be solved in the process Chinese materia medica becoming one of the most important industries in the international market. Studying systems pharmacology and systems toxicology by utilizing complex biological networks, constructing reliable molecular effect and toxicological property networks related to Chinese materia medica targets, reflecting molecular network and toxic mechanism of related biological entity under specific disease state, integrating effect material active target networks and disease biological networks, analyzing relationships between active substance and disease, components and toxicity in “drug-target-disease” networks and “drug-target-activity/toxicity” networks using network topology and dynamics methodology, identifying target combination, pathway combination, subnet combination, drug combination, have highly improved the researching efficiency of Chinese materia medica complex pharmacodynamic substances. Mainly based on studies of Aconitum by the author's group, this article illustrated approach to and methodology of toxicity-activity networks integrated analysis research on toxic Chinese materia medica.