Abstract:With the continuous development of social economy, the state attaches great importance to scientific and technological progress, relying on scientific and technological progress as an important measure to promote economic development, and continue to increase investment in science and technology. Scientific institutions to strengthen budget management,can reasonably control the expenses, effectively allocate resources, improve the use efficiency of funds, and improve the level of budget management, strengthen internal communication and coordination, integration of internal resources, improve scientific research level, scientific research units for the market competition of the inevitable choice. To strengthen the budget management of scientific institutions, and to promote the development of science,and to improve the financial management level of scientific institutions. Based on the theory of COSO internal control, this paper discusses the reasons of the problems in the budget management of scientific research institutes.