By using the literature analysis method, the paper analyzes the defects and demands of electronic medical record(EMR) quality control, establishes a three-level EMR quality control management mechanism, optimizes the hospital information system, focuses on the realization of automatic quality control function. Through the empirical test, the system realizes the closed-loop management of the whole process of medical record data after the optimization, reduces the defects of medical record, and improves the quality of medical record.