As an experimental field for deepening China''s scientific and technological system reform, the organizational innovation and institutional reform of new-style R&D institutions are closely related. From the theoretical perspective of institutional entrepreneurship, the organizational innovation of new-style R&D institutions has been redefined, and a grounded theory method has been used to construct an organizational innovation process model. Research has found that new-style R&D institutions integrate and drive stakeholders externally, establish the identity of "innovation hubs", create new institutional templates internally, and construct and interpret the new identity of "innovation complexes". The two processes dynamically collaborate to jointly shape the new institutional logic that binds technology and economy. A traceable and holistic theoretical explanation for the institutional advantages of new-style R&D institutions has been presented, providing reference and inspiration for establishing and improving modern scientific research institution system and promoting the modernization of the scientific and technological innovation governance system.