Based on the analysis of the institutional change in national research indirect expense,the problems of extrac-ting,using and managing research indirect expense under the new situation are analyzed in this study by taking 985 univer-sities as research objects. The reasons causing these problems are discussed,which include both the internal reasons such as different understandings on research indirect expense and the influence of cost accounting mode in universities on the management of the research indirect expense,and external reasons due to the incomplete supporting policies such as the un-clear accounting content of the research indirect expense,the lack of universities classification management and low ratio of the performance of the spending but short of maximum limit control per person per year. On this basis,some suggestions are proposed in this paper,such as the establishment of the correct understanding on research indirect expense,clearness on the accounting subjects of research indirect expense,reinforcement on the performance evaluation on the researchers,and implementation of differential indirect expense compensation policies,etc.%在分析我国科研间接费用制度变迁的基础上，以985高校为研究对象，分析新形势下高校科研间接费用提取、使用和管理中存在的问题，探讨这些问题既来源于高校和科研人员对间接费用的认识存在偏差、高校的成本核算方式影响间接费用的管理等自身原因，也来源于间接费用政策的核算内容不明晰、缺乏分级分类的差异化管理、绩效支出比例偏低但缺少每人每年最高额度限制等政策配套不完善的外部环境原因。在此基础上，进一步提出树立对间接费用的正确认识、明确间接费用的核算科目、加强科研人员的绩效考核以及实施差异化的间接费用补偿政策等建议。
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