Abstract: As a document recorded by professional medical personnel, electronic medical records contain a large and important clinical resource. How to use a large amount of potential information in electronic medical records has become one of the major research directions. Chinese electronic medical records are knowledge-intensive, in which the data has considerable research value. However, they have more complex entities because of the language features of Chinese, and the composite entity is long. These sentences components in the text are missing. Moreover, the boundaries of clinical entities are often unclear. Labeling corpus is a job that requires a great deal of manpower because of the technical language used in a given text. Therefore, the recognition of Chinese clinical named entities is a hard problem. Considering these characteristics of Chinese electronic medical records, this paper proposed a double-layer annotation model that combined with a domain dictionary and conditional random field (CRF). A medical domain dictionary was constructed by statistical analysis method, and combined with CRF to mark two different granularity labeling operations. The manually constructed medical domain dictionary has extremely high accuracy for the recognition of registered words, and machine learning could automatically recognize unregistered words. This work integrated the two aspects based on these advantages. With the proposed method, diseases, symptoms, drugs, and operations could be recognized from Chinese electronic medical records. Using the test dataset, the Macro-P with 96.7%, the Macro-R with 97.7% and the Macro-F1 with 97.2% were obtained. The recognition performance of the proposed method was greatly improved compared with that of a single-layer model. The recognition effect of deep neural network with attention was also analyzed, which did not perform well due to the size of the domain dataset. The experimental results show the efficiency of the double-layer annotation model for the named entity recognition of Chinese electronic medical records.