With the popularization of computer applications and the development of Internet, the network has grown of very large-scale, and is constantly expanding, which bring a higher demand for secure network management. To make efficient secure management to large-scale network, we design a secure management method based on multilevel agent. We build a multilevel structure for large-scale network, and designed the NMS (Network Management Server) monitor-agent framework. Our method provides real-time response to security incidents and can be used to analyze and forecast threats in network. Especially, it can perfectly handle the dynamic topological changes in large-scale network. Besides, we introduce RSA public key cryptosystem in data transmission process. By encrypting source data before transmission, we achieve the goal of ensuring the confidentiality and integrity of data.