The protection of traditional Chinese medicine knowledge，the current intellectual property rights system，the intangible cultural heritage protection system，and the biodiversity protection system are quite ineffective.The patent system can''t protect the traditional Chinese medicine knowledge in the "public domain"，it has facilitated the biological pirates''crimes instead.The plight of the protection of traditional Chinese medicine knowledge urges proactive protection measures for a wholesome protection.Establishing a special protection system for traditional Chinese medicine knowledge，recognizing the relevant "property rights" of holders of traditional Chinese medicine knowledge，and delineating the rights boundary with the current intellectual property protection system can effectively achieve a balance of interests between holders and users of traditional Chinese medicine knowledge，subdue the conflicts between domestic and foreign patent authorizations，and truly put into effect the legal protection system for traditional Chinese medicine knowledge.