With the reform of China’s science and technology system and the optimization of resource allocation， the scale capacity of scientific and technological innovation in universities is increasing， and the indirect funding of scientific research projects provides an important guarantee for the cost compensation and personnel incentive of scientific research institutions. There are some challenges in the overall management of indirect cost of scientific research in universities. It systematically combed the changes in the policy of indirect cost of scientific research in China， compared the distribution patterns of indirect cost of scientific research in 20 universities， and analyzed the existing problems and causes of overall management of indirect cost in universities. It puts forward some suggestions on how to enhance the efficiency of scientific research indirect cost management from the aspects of science and technology plan and project management， indirect cost distribution， science and technology management system of colleges and universities， scientific research cost accounting and personnel salary system reform.