Objective To determine root causes in medication errors and to integrate them into electronic adverse safety event reporting system, thus to achieve automatic and structured analysis of root causes in medication errors. Methods Using root cause analysis, the research team summarized root causes of medication errors and developed consultation questionnaire, then conducted a tworound expert consultation using the Delphi process to determine the information items of root causes. At last, software engineers designed a structured module to report root causes of medication errors in electronic adverse safety event reporting system. Results The root cause module included 18 evoked questions and 84 cue answers. The electronic reporting system contained reporting and chart modules which had query and analysis function. Conclusion The root causes cover main factors in quality management of medication error. The reporting system helps managers fastly and effectively understand root causes in medication errors, thus to take targeted measures and enhance work efficiency and efficacy.