Taking public Internet security requirements as a background, the study of network cooperative defense is based on community structure. First, according to the logical structure and node function of the network, the target network is divided into several network communities, and a basic communication model of cooperative defense architecture is designed according to the distributed cooperative control mode. On this basis, a cooperative network defense architecture based on community structure is proposed by integrating information honeypot and honeynet, cooperative defense strategy library, and firewall based on the node trust value management. A cooperative mechanism is designed by using the experience of concept of network ecosystem operation for reference. Through the collective activities as situation awareness, the situation analysis, the action decision and the regulation feedback, the network defense abilities, such as virus detection, rapid response and emergency recovery, can be improved respectively. Finally, taking the latent virus defense as an example, the cooperative network defense flow is given as well as numerical performance simulations. Compared with the noncooperative defense network, the network cooperative defense based on community structure can inhibit the spread of latent virus and enhance network security with less communication loss.