Abstract: Focusing on the management reforms of government expenditure for science and technology,this paper illustrates the significance of indirect cost reimbursement mechanism of funds for scientific research. It carries out comparative studies on this issue with overseas universities,analyzing the reforms and characteristics of indirect cost reimbursement in government funded scientific projects in our country. It proposes corresponding measures from the perspectives of accounting of costs for managing school resources,strengthening budgets management and appraisals of funds,as well as improving the evaluation of the performances of funds for scientific research. Targeting the current state of the allotments of resources in research universities,the paper puts forward an accounting model for the costs of public housing. The results show that it has not only regulated resources effectively but also played a prominent role in dealing with indirect cost reimbursement in government funds for scientific research.