Innovation of inter-organizational cooperation is an important model for open innovation.It is an important way for innovative enterprises to reduce risk and to access external knowledge which means it is an urgent task to conduct a study.In the inter-organizational cooperation innovation process, external organizations network management would become a key when the organization is highly dependent on other organizations to provide new technology.So we analyzed the process of inter-organizational cooperation and innovation in the software industry which shows that the key for enterprise innovation is to access external inter-organizational flow of knowledge.We also found that the depth of the network co-operation and management of external organizations help to provide knowledge and resources for business innovation and the breadth of the organization and cooperative relation help the enterprises to find new technologies and markets.On this basis, we build innovative model of cooperation between the enterprises organizations.