Abstract: According to the stage characteristics of R&D investment, we divide it into two kinds: research investment(R，including basic and applied research) and experimental development investment(D). By using the panel data of China’s listed manufacturing companies, we divide them into different financing constraint categories and study on the effects of financial capital and government subsidy on two kinds of R&D investment. We get the conclusions that: The comprehensive promoting effects of government subsidy on R&D investment is higher than that of financial capital on it; The promoting effects of the two kinds of external financing on the experimental development investment is prominent, but the promoting effects of them on the research investment are not prominent; The positive effects of government subsidy in easing the financing constraints are more effective on private and innovative enterprises. The key to solving the problem of the shortage of the enterprises’ investment on basic and applied research is to upgrading the financial function and improving the capital allocation efficiency.