Abstract:This paper taking Y Research Institute directly under the Ministry of Agriculture and Rural Affairs as the research object, and analyzes the current status of budget performance management of scientific research funds in Y Research Institute. At the same time, taking a public welfare scientific research project of the Institute as a case, this paper specifically analyzes its budget performance management process and existing problems, especially for the performance indicators, the analytic hierarchy process (AHP) is used to redistribute its score weight. The results show that: the performance evaluation of public welfare projects should focus on social benefits, sustainable development, public satisfaction and other aspects.