Purpose/Significance To construct a Chinese electronic medical record (EMR) annotation system, so as to realize the automatic annotation of EMR texts. Method/Process The system requirements are analyzed, and the system architecture is elaborated. The system is introduced from 3 aspects: the data layer, the service layer and the functional layer, including user authority management, entity and relation annotation processes, and annotation algorithms, etc. Result/Conclusion The Chinese EMR annotation system can effectively meet the requirements of the EMR annotation task and has been successfully applied to the construction of pituitary adenoma EMR corpus.