Internal governance and salary system have significant impact on the development of research institutes. Internal governance is the cornerstone of scientific research institute’s management，which involves the organizational structure，power allocation，decision-making mechanism and supervision mechanism of scientific research institutes，directly affecting their operational efficiency and innovation ability. A sound internal governance system can ensure the orderly progress of scientific research activities，promote the rational allocation of scientific research resources，and improve the quality and efficiency of scientific research. The salary system is the core mechanism for motivating researchers in research institutes，and its reasonable design directly affects the enthusiasm and innovation motivation of researchers. A reasonable salary system can attract and retain outstanding talents，stimulate the innovation enthusiasm and work motivation of researchers，and promote scientific and technological innovation and achievement output in research institutes. Therefore，this study focuses on the internal governance and salary system reform of research institutes，provides theoretical support and practical guidance for the modern management of research institutes by analyzing the current structure and mechanism of internal governance in research institutes，as well as the operation and reform trends of salary systems.