Abstract: Based on a comparative study of China and the U.S. R&D expenditures in 1980s and 1990s, this paper has started a re-comparative study of China and the U.S. R&D expenditures since 1990s.The study finds that, although the scale of China's R&D expenditure (investment amount and intensity ) has been significantly changed, while there are still great differences in R&D investment structures and sources: America still attaches great importance to basic research, but in our country it doesn't; In the United States, the Research and Development expenditure is mainly supported by the federal government, while in China, local governments R&D expenditure not only keep highly consistent with central government, but also rise significantly. the United States R&D investment based on the theory of market failure, while China is more based on the “ZhongShi”theory(paying more attention). In the contexts of public finance expenditure performance increasingly attracts much public attention, this paper suggests that China should work out the theoretic innovation on the role of market and government to optimize R&D expenditure theory; further stabilize the scales of R&D expenditure, with the further improvement of Science and Technology statistic , adjust to optimizing the structure of R&D expenditure, and strengthen basic research expenditure, local government should explore the suitable scales and scientific modes of R&D expenditure, and gradually reduce the direct subsidies.