This paper studies Natural sciences Academic research level Appraisal method. first, Reference a large number of relevant scientific research index system literature, propose level of scientific research of natural science disciplines comprehensive evaluation index system. And using network analysis (ANP) and factor analysis to the level of scientific research on these subjects to rank college and analysis. Finally, we use the combination of ANP and factor analysis assigning weights to the weight of two methods reasonably together. In this paper we make a simple plan, the minimum deviations squares as the objective function， comprehensive evaluate existing 10 universities part academic research level, access to comprehensive score and ranking.