This paper put forward a construction mode of ancient books protection system for special library of traditional Chinese medicine based on the survey and analysis of ancient books protecting status. With the working experience of protecting ancient books in our library, we studied the technical system and organization system for ancient books protection, listed out the standard of technical system and content of organization system, and formed an ancient books protection system for special library of traditional Chinese medicine. This system included scientific technology, advanced methods, effective management, orderly operation and right-hand protection, which can be widely applied in our industry to promote benign and sustainable development of work in ancient books protection.