Abstract:Although having implemented several adjustments, the management of scientific research funds in China has not maximize the promotion of scientific innovation yet, for the essential reason that the reform of management of scientific research funds have never been connected with the institutional management system. At present, the movement of the management of scientific research fundsis restricted to the institutional management system, such as the establishment management, merit-based salaries, the governmentSprocurementSsystem and the centralizedStreasurySpayment system, leading to the lack of autonomy in the use of scientific research funds. This paper struggles to analyzing the deep-seated contradictions between the provisions of our institutions and the management of scientific research funds in order to find out the institutional factors in the reform of R D funds which is difficult to break through. Then we make some suggestions to go further on the reform of the scientific research institution and scientific research funds.