In the late 20th century, the rapid development of life sciences resulted masses of biological data, in which laws of life sciences urgently needed to be excavated. Together with the progress of computer science and technology, bioinformatics was born. Chinese medicinal resources, especially the plant resources, are the basis for the development of the Chinese pharmaceutical industry. As a new discipline and important life science research tools, bioinformatics applied rapidly in the study of Chinese medicine resources and involved in different aspects of genomics in recent years. Bioinformatics provides a new research approach to reveal the biological principles, methods and techniques and powerful tools of excavation, at the same time it is speeding researches in the field of Chinese medicine resources and the development of the industry. This article summarizes a comprehensive collection of bioinformatics application data in the study of Chinese medicine resources, prospects the application in Chinese medicine resources, and provides a basis bioinformatics information for the study of Chinese medicine resources.