Abstract: This paper estimates the R&D capital stock in manufacturing industry in the framework of SNA, which could provide more reliable data for subsequent economic analysis. Firstly, we use auxiliary indicators and statistical tests to estimate and adjust R&D expenditure and its composition, and solve the problems of industry classification and statistical range; Secondly, within the framework of SNA(2008), this paper transforms R&D expenditure to R&D investment, and uses BEA approach to estimate the R&D capital stock in 28 two-digit manufacturing industries from 1990 to 2016; Finally, a further comparative analysis is made to put forward targeted policy recommendations. The results show that the R&D capital stock in manufacturing industry has a rapid growth; the high-tech industry represented by computer, communications and other electronic equipment manufacturing is the main force of scientific and technological innovation but it has no obvious effect on basic research and traditional manufacturing; some industries of traditional manufacturing have been the new growth points of R&D capital stock although the contribution of traditional manufacturing has been decreased.