Research institutes are an important component of the national innovation system construction. At present, state-owned research institutes mainly implement the system of institute director responsibility under the leadership of the Party committee, while non-state-owned research institutes mainly adopt the system of institute director responsibility under the leadership of the board of directors. To achieve the transfer and transformation from science to technology, and from technology to industry, it is necessary to accelerate the exploration of new management systems for research institutes and improve their governance systems. From a management perspective, the main problems existing in research institutes have been identified, manifested as a lack of structured decision-making mechanisms, incomplete governance systems, poor integration with market factors, difficulty in accessing social capital, and poor achievement transformation. It has been proposed that for different types of research institutes, the core governance concept of enterprise management can be used as a reference to construct a governance framework for "SAER" structured management, improve the mechanism of structured management, establish a council or strategic guidance committee, fully leverage the role of academic and evaluation committees, and open up effective channels for connecting with market resources. At the same time, it is pointed out that the role of the Party committee in directing and managing the overall situation should be leveraged to achieve optimal management efficiency and maximize scientific research output.