Abstract: Object To establish and apply an evaluation method based on DEA in NSFC project performance evaluation. Methods Based on the analysis of NSFC projects in Peking University People's Hospital,this paper determined the evaluation index system of NSFC projects.The outputoriented DEA was selected and applied in the performance evaluation.Results We figures out the DEA ratio of every NSFC project with the established method in the program of DEAP Version 2.1.Conclusion The method based on DEA can reflect the performance of NSFC projects,and the evaluation results can provide project managers and the management department of NSFC with evidences and references to make polices for project management.