Based on the interoperability analysis of electronic medical record system, the paper introduces HL7 CDA clinical file standard and the advantages of using XML technology based on this standard for medical documentation describing. According to the features of structured electronic medical record, it points out the design of clinical sci-tech research application system with electronic medical record as the core. Structured electronic medical record provides more accurate and efficient information retrieval and analysis functions for medical sci-tech research, it’s the future direction of development of electronic medical record.