Recently, major scientific and technology projects have been important measures to promote the development of economy and technology. As more and more organizations are involved in the projects, collaborative management is necessary. This paper introduces the formation of organization interfaces of major scientific and technological projects. We see all organizations the project involves as a system, through the analysis of such a complex system, making sure six main factors influencing system collaborative operation, such as organizational effectiveness, resource sharing. On the basis of the six factors, author found the model of organization interfaces synergetic management. At the same time, the thesis analyzed the operational mechanism and concrete methods of the model.