For further analysis and research of traditional Chinese medicine pharmacovigilance in Ben Cao Gang Mu (Compendium of Materia Medica)， we designed a database system based on Jinling version of the Ben Cao Gang Mu. Firstly， the paper expounds the requirements of database establishment and selection of storage model. Then it introduces the design of concept and logic of the pharmacovigilance database， and explains the structure and data flow of the knowledge discovery system based on this database. Finally the paper lists some researches on the safety of prescribing Chinese medicine that can be done with the application of data mining algorithms.