Abstract:As an embedded organization, new R&D institutions have the characteristic of diversified investment entities. This collaborative innovation organization is essentially a multi-dimensional transaction relationship linked by direct and indirect interaction, and a relationship contract of multi subject collaborative interaction. Aims to explore the formation mechanism of organizational embeddings in new research and development institutions, this research constructs a relational contract structure analysis model consisting of relational embedding structure and contract governance structure, suggests that the embedding methods of new R&D institutions are positive embedding and reverse embedding, the manifestations are property rights relationship, structural embedding, and institutional relationship, the evolution stages are the initial stage, growth stage, and maturity stage, also proposes differentiated features in embedded forms for different stages. Then, based on the binary perspective of "subject process", this research provides a theoretical explanation of the embedded organizational paradox that appears in the development practice of new R&D institutions, and proposes solutions from the perspectives of relationship quality and relationship position.