To solve the problems in traditional network protocol recognition methods, such as difficulty of manual feature extraction and low recognition accuracy, an application protocol recognition method based on Convolutional Neural Network (CNN) was proposed. Firstly, the raw network data was divided according to Transmission Control Protocol (TCP) connection or User Datagram Protocol (UDP) interaction, and the network flow was extracted. Secondly, the network flow was converted into a two-dimensional matrix through data prepocessing to facilitate the CNN analysis. Then, a CNN model was trained using the training set to extract protocol features automatically. Finally, the trained CNN model was used to recognize the application network protocols. The experimental results show that, the overall recognition accuracy of the proposed method is about 99.70%, which can effectively recognize the application protocols.