Abstract: According to Aghion(2005), enterprises’ cyclic structure of short and long term investment is different. Based on his theory, we build a theoretical model under imperfect capital market in which government subsides ease financing constraints and thus affect the cyclicity of R&D investment. Using panel data of 1580 listed manufacturing enterprises during the period 2007~2014, we conclude that: (1) There exist universal financing constraints in manufacturing enterprises in China, and state-owned enterprises suffer more financing constraints than non-state-owned enterprises; (2) Due to imperfection of capital market and external financing constraints, enterprises' R&D investment shows procyclicaity when we use state-owned enterprises, non-state-owned enterprises and all samples, and the procyclicality of R&D investment is more obvious in non-state-owned enterprises than in state-owned enterprises; (3) Government subsidies can alleviate financing constraints and the procyclicality of R&D investment to a certain extent. The effect of government subsidies is more obvious on non-state-owned enterprises than on state-owned enterprises.