Abstract: Adopting the grounded theory approach, this paper selects five new R&D institutions as the research objects, constructs an analysis framework of "embedding motivation-embedding path-embedding effect" to study the behavioral motivations and implementation mechanism of new R&D institutions embedding national strategic scientific and technological forces,and proposes countermeasures and suggestions to promote industry university research cooperation from the perspective of management practice. The result indicates that environmental embeddedness and bilateral embeddedness are the behavioral motivations of organizational embeddedness of R&D institutions, cognitive embeddedness, relational embeddedness, and social embeddedness are the main paths for new R&D institutions to embed national strategic scientific and technological forces, ecosystem optimization, agglomeration of innovative forces, guarantee of innovative factors, and economic and social benefits are the embedding effects.The embedding of both parties is the result of dynamic evolution of their behavior, characteristics of self-organization, adaptation, and self circulation are presented. The degree has a significant impact on the effectiveness of embeddednes, and needs to be continuously debugged and optimized in practice.