Abstract: New R&D institutions, as the testing ground for China's science and technology system reform, have become an important regional innovation force in the bustling construction at the local level. However, the core question of where exactly the 'newness' of these institutions lies remains to be further studied. Grounded in the national innovation system and from the perspective of institutional economics, the article conducts theoretical analysis on new R&D institutions using the concept of transaction costs, and summarizes the institutional models of these institutions in practice through multiple case studies. The research indicates that new R&D institutions innovate through institutional integration, reducing the institutional transaction costs of innovation activities, and increasing the incentive levels for science and technology personnel, thus supporting integrated functional innovation with common technology services and technology transfer incubation as its core. Based on the classification of institutional models, new R&D institutions in local practices exhibit four types: basic research type, technology service type, technology incubation type, and product development type, among which basic research type and product development type institutions deviate significantly from the standard model. This research provides important reference for clarifying the conceptual positioning and functional boundaries of new R&D institutions, and offers important experiential insights for the optimization management of future new R&D institutions.