This paper discusses the application of deep learning technology in computer network security maintenance in detail， systematically expounds the basic theory and specific application scenarios， and designs a computer network security maintenance system scheme based on deep learning， which not only includes deep learning modules for intrusion detection and malware detection. The design concept and implementation details of multi layer security defense architecture are described in detail， as well as the importance and implementation strategies of data encryption and privacy protection. Through the deployment and maintenance of the system， the paper shows the method of deep learning to improve the security protection capability in the actual network environment， and finally verifies the effectiveness and practicability of the design through the system test.