In recent years, Chinese government has been increasing its support for the scientific and technological activities of enterprises. At the same time, the rationality, effectiveness and efficiency of the government's public scientific and technological resources investment have been questioned. Whether government innovation support is beneficial or hinders the innovation of enterprises has been discussed in the past, but the conclusions are not consistent. From the viewpoint of institutional logic, governments in emerging economies have a key impact on regulatory policies and control of scarce resources, and tend to think that government innovation policies will have a positive impact on enterprise innovation. From the viewpoint of efficiency logic, it is believed that government innovation policy will produce principal-agent problem, which is not conducive to enterprise innovation. Our research integrates the efficiency logic (agency theory) and the system logic. This research uses the Chinese enterprise innovation database and takes Anhui science and technology enterprises as samples from 2011 to 2013. It finds that in emerging economies, government innovation support policies enable enterprises to obtain key R&D resources, but reduce the efficiency of enterprises using these resources for innovation. In this case, there is an inverted U-shaped relationship between the integration of institutional logic and efficiency logic, innovation support policy and enterprise innovation. In addition, the study also finds that different types of government innovation support have different impacts on enterprise innovation, and the nature of property right has a moderating effect on the relationship between government innovation policies and enterprise innovation.