Taking traditional Chinese medicine （TCM） as the main body， integrating modern medical research results and technology methods， innovating clinical diagnosis and treatment mode， and enriching the theoretical system are important directions for the innovative development of TCM at present. However， there are still two key problems to be solved in the process of innovative development of TCM under the background of modern medicine. On the one hand， the traditional syndrome differentiation and treatment mode of TCM is difficult to integrate with modern cli-nical diagnosis and treatment of diseases； on the other hand， the macro syndrome differentiation and treatment in TCM cannot accurately dock with the microscopic physical and chemical indicators of modern medicine. Therefore， in this paper， we innovatively put forward the theoretical framework of “two reconstructions”，i.e. reconstruction of diagnostic and treatment system and materia medica system in modern Chinese medicine， and systematically explain its connotation， purpose， method and significance. We advocate that by learning from the cognition of modern medicine diseases， inheriting the disease examination thinking of TCM， and classifying and staging modern diseases in the way of TCM， the modern TCM diagnosis and treatment system can be reconstructed. At the same time， we also advocate that by absorbing the results of modern pharmacological research， integrating the understanding of the efficacy of Chinese material medica， and constructing the theoretical framework of dose-response relationship in TCM prescription， the reconstruction of modern Chinese herbal medicine system can be completed. On the premise of inheriting and carrying forward the advantages of TCM， the realization of “two reconstruction” can break through the limitations of traditional treatment based on syndrome differentiation and improve the accuracy of clinical diagnosis and treatment of modern diseases ， which is an important path to the preservation and innovative development of TCM.