Abstract: Collaborative innovation of Mission-oriented interdisciplinary scientific research organizations is an important way to form a strong synergy of key core technologies. Based on the in-depth interview data of 5 interdisciplinary organizations responsible for and participating in the Chinese Academy of Sciences' strategic pilot project, the research applied grounded theory to construct a three-dimensional Mission-oriented interdisciplinary scientific research organization's collaborative innovation impact. A factor analysis model is used to explore thepath that is conducive to the collaborative innovation of Mission-oriented interdisciplinary scientific research organizations. The research shows that:organizational characteristics and the operating mechanism of organizational management are internal factors that affect the collaborative innovation of Mission-oriented interdisciplinary scientific research organizations; collaborative motivation, collaborative willingness and collaborative ability are the core factors that affect collaborative innovation among organizations; including policy support, technical standards The institutional environment, including the environmentand the intellectual property system, is an external factor that guarantees the collaborative innovation of Mission-oriented interdisciplinary scientific research organizations.