National scientific research institutions are an important component of the country's strategic scientific and technological strength, and an important carrier for leveraging the advantages of the new national system. In the new era, national scientific research institutions shoulder the mission of undertaking strategic basic research and tackling fundamental scientific problems related to core key technologies. The funding mechanism is an important mechanism to ensure the effective play of the strategic scientific and technological strength of national scientific research institutions, and it is also a breakthrough and foothold to enhance the investment efficiency of national scientific research institutions. Since the reform of the science and technology system in 1985, China has established a "stable+competitive" funding mechanism for national scientific research institutions, effectively stimulating their vitality. However, in the face of the current complex and ever-changing international situation, the central tasks of comprehensively promoting the construction of a strong country and the great cause of national rejuvenation, as well as the strategic goal of building a science and technology strong country by 2035, the funding mechanism of China's national scientific research institutions still has problems such as multiple and fragmented funding channels, limited autonomy in internal fund allocation at the institutional level, and an incomplete evaluation mechanism for funding efficiency, which need to be further improved. The prominent problems faced by the existing funding mechanism include the investment mechanism, internal configuration mechanism, and evaluation mechanism for investment effectiveness, which are important components of the funding mechanism for national scientific research institutions. The improvement of investment efficiency should be guaranteed by efficient investment mechanisms, reasonable internal allocation mechanisms, and effective investment evaluation mechanisms. From the above key aspects, it can be seen that the current funding mechanism for national scientific research institutions in China has the following problems. One is that the existing investment mechanism is difficult to support the needs of national scientific research institutions to focus on specific issues and tackle them in an institutionalized manner. The funding for China's national scientific research institutions mainly comes from stable institutional operating funds and competitive project funds. From the current reality, stable institutional operating funds are mainly used for basic operating expenses such as water, electricity, heating, and paying some personnel salaries, while the funds required for conducting scientific research activities mostly come from competitive project funds obtained from multiple channels. This investment mechanism is difficult to encourage national research institutions to fully leverage their organizational advantages in institutionalized scientific research. Although special research funds such as the Knowledge Innovation Program of the Chinese Academy of Sciences and the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences have effectively alleviated the instability of funds for competitive projects of national scientific research institutions, the above mechanism has not been transformed into a long-term mechanism, which is difficult to fundamentally solve the problem of investment mechanism of national scientific research institutions. Secondly, in the allocation of internal personnel funds, there is pressure for scientific researchers to raise their own salaries, which makes it difficult for them to devote themselves to pursuing long-term research goals. The three yuan salary system is the main body of the salary mechanism for personnel in China's national scientific research institutions, consisting of three parts: basic salary, position salary, and performance-based salary. Among them, the basic salary and some position salaries are paid by the operating funds of stable support institutions. Overall, the salary level paid by stable support institutions for operating expenses is relatively low, and its proportion in the total salary is limited. As the main part of the three yuan salary, performance-based pay needs to be self raised by researchers. In order to obtain performance-based pay, there have been problems such as researchers taking on too many competitive funding projects and projects that do not match the mission positioning of their institutions. Although national scientific research institutions such as the Chinese Academy of Sciences have guaranteed the salaries of some scientific researchers through special research posts, reducing the pressure of self financing performance pay for scientific researchers. However, overall, researchers in national research institutions still face pressure to self fund their salaries, making it difficult for them to focus on pursuing long-term research goals. Thirdly, an effective mechanism for evaluating the effectiveness of capital investment has not yet been established. The evaluation of the effectiveness of funding investment in national scientific research institutions is an important measure for national scientific research institutions to implement the requirements of the Party Central Committee and the State Council for comprehensive budget performance management. However, due to the management path dependence problem of block segmentation, the current budget performance evaluation of national scientific research institutions is mostly limited to performance evaluation from a financial perspective, and has not yet been organically integrated with the institution's mission positioning, performance goals, strategic planning, scientific research organization, etc. The existing comprehensive scoring system is difficult to answer the question of the effectiveness of funding investment in national scientific research institutions. Starting from the key links to improve investment efficiency in the new era, in order to better leverage the advantages of the new national system and fully utilize the strategic scientific and technological strength of national scientific research institutions, we can start from the investment mechanism, personnel salary allocation mechanism, and investment effect evaluation mechanism, improve the funding mechanism, and enhance investment efficiency. One is to establish an investment mechanism that is coordinated with the institutionalized organizational mechanism of national scientific research institutions. Simplify investment channels, draw on the experience of international directional competition and other investment mechanisms, and allocate a portion of the project funds that currently need to be obtained through competition directly to national research institutions with research conditions and capabilities, in order to increase the proportion of stable support funds for institutions. The increase in the proportion of stable support funds can effectively leverage the subjective initiative of national scientific research institutions in fund allocation, lay a solid foundation for institutionalized scientific research organizations, and provide conditions for further solving internal fund allocation and evaluation mechanism problems in national scientific research institutions. The second is to establish a salary and incentive mechanism that helps researchers focus on their research with peace of mind. Regarding the issue that the main part of the salary for personnel in national scientific research institutions, performance-based pay, mainly comes from indirect project costs and performance rewards, we can take advantage of the opportunity of the pilot reform of the salary system in scientific research institutions to broaden the compensation channels for performance-based pay and increase the proportion of basic salary and position salary in the total salary. The third is to establish a national research institution investment efficiency evaluation system based on budget performance evaluation. In response to the repeated performance evaluation of "things" in the current practice of budget performance evaluation of national scientific research institutions, and the lack of evaluation of investment efficiency and effectiveness, it is necessary to effectively implement the reform requirements of comprehensive implementation of budget performance management. Based on the 3E theory of technology budget performance evaluation, a new budget performance evaluation system focusing on investment efficiency evaluation and effectiveness evaluation should be constructed to answer the question of investment efficiency of national scientific research institutions. (New Society)