Abstract: Contemporary science and technology have shown unprecedented institutionalized characteristics. A new notion of “institutionalized science research” is introduced in the context of policy necessary, and its distinctive characteristics are explored from historical logic, theoretical logic, and empirical logic. This study demonstrates that the history of scientific development is also the history of scientific knowledge production and scientific institutional evolution. Improving the efficiency of scientific research is the intrinsic motivation for the evolution of institutionalized science. Knowledge production mode II cannot be simply used as a basis for the transformation of research institutes. Knowledge innovation advances by interaction in the two-way as highly split and integration of scientific disciplines, which reflects the evolution of institutionalized science research. The knowledge system shapes matching research organization. The knowledge domains that play a leading role in the knowledge system architecture are different, forming a macro dynamic evolution of institutionalized science research history. As revealed by the experience of some famous scientific research institutions, scientific research innovation is not achieved in isolation, but requires an interaction between science, technology, and instrument development. Mutual support between traditional and cutting-edge disciplines is also important. Organizational design should take into account both the concentration and integration of scientific research. These structural resource allocations are the irreplaceable value of the institutionalized science research. This article provides a new perspective for research on science and technology policies, and has theoretical and practical reference value for the future reform of China’s science and technology system.