The purpose of this paper is to calculate the weight of performance measures for evaluating sponsored research of Department of Healthy, Executive Yuan. The indicators that be used were designed by National Science Council, and those indicators generated as a hierarch structure, so AHP could be used when deciding the weight of performance measures. This paper demonstrated the calculating process, and experts' opinions were the base for AHP. The results of this paper could be the reference for Department of Healthy when they design the evaluating system for sponsored research.