Abstract: Developing well-coordinated policy measures to enhance policy synergy is the key to improving the macro-economic governance system. Under the endogenous R&D framework, a dynamic stochastic general equilibrium model was constructed. The model included residents, manufacturers (including green R&D manufacturers and non-green R&D manufacturers), and government departments to study the impact of three green policy shocks, namely government green R&D subsidies, carbon emission reduction subsidies, and environmental governance investments, on environmental and economic variables such as total carbon emissions and carbon emission intensity. The study focused on the combination of carbon emission “dual control” policies. Simulation analysis found that: (1) three green policies had short-term negative and long-term positive effects on total social output, and the win-win goal of growth, carbon reduction, synergy and efficiency improvement could be achieved. Moreover, green R&D subsidies had the most significant positive peak effect on total social output. (2) Environmental governance investment and carbon reduction subsidies only suppressed the total carbon emissions in the short term, and their output effects would increase the total carbon emissions in the long term. At this time, it was necessary to coordinate with green research and development subsidy policies to reduce carbon emissions. (3) The government’s three green policies could all reduce carbon emission intensity, but in terms of effectiveness, green R&D subsidies was the most effective method, while government environmental governance investment and emission reduction subsidies had little impact on carbon emission intensity. Increasing subsidies for green research and development to encourage green research and development was the most favorable policy tool for achieving dual control of carbon emissions and carbon intensity. (4) The three green policies had a crowding out effect on the main macroeconomic variables, but a reasonable combination of policies could balance economic growth, dual control of carbon emission intensity, and improvement of ecological environment quality. According to the research findings, it was suggested that carbon emission reduction subsidies should not become a long-term policy, and the government should reasonably match the two policies of environmental governance investment and green research and development subsidies.