From the perspective of the heterogeneity of enterprise organization system (including enterprise decision-makers and resources endowment), this study investigates the effect of government subsidy to the R&D investment by using the listed companies of GEM in China from 2010 to 2013 as samples. The empirical results show that government subsidies to the R&D investment has significant positive correlation; CEO power positively moderates the effect between government subsidies and R&D investment; enterprise scale and technology staff ratio also positively moderate the effect between government subsidies and trade investment. In order to further promote enterprise innovation research and development activities, the subsidy policy of government needs to tend to those companies of GEM which tend to independent research and development innovation in the business decisions and resource endowment structure.