The first step in this paper is to use TOPSIS method to evaluate the scientific research output of humanities and social sciences in public undergraduate universities of central area of China. The results show that the overall research output is not satisfacto- ry,the gap is larger. And then the system generalized moment estimation method is applied to analyze. The empirical results indicate that the contribution of scientific research input to research output is not high for humanities and social sciences,while the contribution of R & D expenditure is greatest. In terms of contribution to scientific research input,the overall situation of Hubei province is the best, the overall situations of Jiangxi and Anhui province are poor; the overall situations are better for comprehensive universities,normal uni- versities,financial and economical universities. Conversely,the overall situations are poor performance for agriculture and forestry uni- versities,medical universities and other universities. In addition,the overall situation is the best for 985universities and the overall per- formance is poor for other public universities.