Evaluation is indispensable to the effective management of research institutions,especially the efficiency assessment is so important that it can compel the institutions to best their resource utilization.The problems usually encountered in the evaluation process,such as the selection of the indicators,the combination of quantitative and qualitative evaluation method and the explanation of the evaluation outcome etc are analyzed.Regarding these problems,the fuzzy DEA with preference information model is presented.It makes use of the fuzzy method to preprocess the quantitative data and the qualitative information.Based on the fuzzy data,the DEA with preference information model in practice is tested.The result shows that since this model can have a deeper insight into the institution efficiency analysis,it is better than standard DEA models.