Systematically combing the origin and characteristics of the classification style of contents in ancient traditional Chinese medicine （TCM） books through the ages， this article put forward that the emergence of the classification by category system for medical books in the Song Dynasty had become a reference for the classification medical book categories in later generations； under the influence of Neo Confucianism， the compilers of medical books in the Ming Dynasty applied the classification method of outline， which made the content of medical books well-organized and hierarchical， and according to the needs of systematic compilation of medical books and different compilation purposes， the classification logic of various medical books had been continuously improved， and breakthroughs had been made in the format， which improved perfecting the development of classification style in ancient comprehensive TCM books； the application of the body part classification method in the compilation of medical books in the Qing Dynasty made the classification of books more rigorous and organized， and the classification system of various medical texts became more mature. By systematically sorting out the characteristics and origins of the classification system of ancient TCM books throughout history is of great significance for comprehensively understanding of the development of ancient TCM books style and the promotion of the collation， protection and use of ancient books.