Self-reliance in science and technology is the primary requirement for China′s development. In the context of the current tight fiscal policy, government investment in basic research has increased rather than decreased, which fully reflects the urgent need to improve the level of original basic research in China. However, the current scientific research organization based on competitive projects obstructs the improvement of the overall level of basic research. Firstly, the project-oriented scientific research organization does not conform to the scientific rules of basic research. Basic research is exploratory and highly uncertain, researchers tend to apply for projects with research basis in order to finish the project on schedule, which makes it difficult for original basic research to obtain support. Secondly, the current competitive funding is not conducive to original basic research, the research institutes lack self-governance right, and the stable funding for scientists is relatively small, which restricts the innovation vitality of the institutes.This paper constructs the theoretical framework of the two-tier governance system of the basic research institutes, and explains the theoretical logic of the two-tier governance system from the outer administration governance and the inner institute governance. On the basis of clarifying the rights and responsibilities of institutes, the government supports the autonomy of scientific research institutes. As an independent research platform, the institutes form an independent self-governance mechanism with scientists as the core. The government provides long-term and stable research funding to institutes, and entrusts them  with the rights to allocate and use research funding freely, and to recruit and evaluate scientists independently. At the same time, it is clear that the institutes are responsible for making breakthroughs in basic research and innovation, and the government will carry out an overall performance evaluation on the innovation capacity of the institutes to ensure the efficiency of stable funding. Institutes construct a scientists-centered governance model, which includes three aspects: (1) the selection and employment mechanism; (2) the training and support mechanism; and (3) the incentive and restraint mechanism. Finally, the institutes′ governance system is constructed which has clear rights and responsibilities on the outer layer and systematic governance on the inner layer and synergistic effect exists between the two layers, and the system can effectively promote the development of basic research institutes.On the basis of theoretical analysis, this paper takes the successful experience of National Institute of Biological Sciences, Beijing (NIBS) as a typical case, analyzing the functions of the government and institutes in the governance system respectively. Complying with the law of basic scientific research, the government started a pilot project on NIBS. The government applied de-administration on the institute as well as long-term and stable financial research funding. The institute formed an independent governance mechanism, including steady support for scientific research teams, principal investigator in charge, allowing scientists to decide the scientific topic of the research team, improving the income of scientists, building strict peer review evaluation and elimination mechanism, etc. The government and institutes work together to support original basic research breakthroughs and release the innovation vitality of the institutes, which verifies the effectiveness of the two-tier governance system of basic research institutes.The research conclusion includes: (1) The project-oriented basic research organization limited the supporting effect of the funding. It is necessary to establish a two-tier governance system of institutions. (2) The logic of the two-tier governance system of basic research institutes is that the government in the outer layer provides the institutes stable funding, and ensures the institutes fulfill their innovation responsibilities. Institutes in the inner layer construct a scientist-centered governance model, which includes selection and employment mechanisms, training and support mechanisms and incentive and restraint mechanisms. The council system can play the supporting and feedback role between two layers. (3) The successful practice of NIBS can verify the effectiveness of the two-tier governance system of basic research institutes. Finally, this paper puts forward the following practical suggestions: (1) The government should promote the new system of basic research institutes. (2) The government should give research institutes rights of system reform and innovation and carry out institutes′ internal governance mechanisms. (3) The government should increase the proportion of stable financial support for basic research and research institutes and ensure steady funding for researchers. (4) Institutes should establish an effective scientist′s incentive and evaluation mechanism to give full play to researchers′ innovation enthusiasm.