By using DEA-Tobit , we empirically analyze the influence of the stock and the structure of the human capital on regional R&D efficiency in the whole country and the three regions. It shows that the human capital stock and the senior level human capital have significant effect on the efficiency of R&D in the whole country and the eastern region, but this is not true in the middle-western region. Therefore, it is important to strengthen the accumulation of human capital in order to improve the R&D efficiency in the central and western regions.