Based on the concept of narrative evidence-based medicine, this paper elaborates the research design of clinical trial and medical record of traditional Chinese medicine （TCM） in the treatment of functional gastrointestinal diseases （FGIDs） in order to improve and optimize the clinical trial and medical record of Chinese patent medicine treating FGIDs. Combined with the design of clinical trial and medical record of a randomized controlled multi-center trial for FGIDs, it analyzed the items selection and its purpose of the trial design and the medical record mode for FGIDs so as to establish the best design and mode of today. The design of research medical record should be in accordance with the research objective which is principal for the design. The clinical efficacy evaluation method is the key scientific problem in the study of TCM. Therefore, theoretically and practically, this study explores the clinical trial design and the research medical record for dysplasia in the expectation of a better clinical efficacy evaluation method. The core indicators of FGIDs should be discussed for the future study of TCM in the treatment of FGIDs.