Under the premise of limited enterprise innovation resources, the necessary condition for companies to innovate carbon technology is that its revenue is greater than other types of innovation activities. In this essay, author introduced low carbon technology innovation opportunity cost into traditional A-J model, system analyze the impact of carbon tax, carbon emission standards, emission reduction subsidies and carbon emissions permits four environmental policy instruments on the choice of enterprise innovation. The model result shows that each environmental policy tool has an optimal level, but each tool has a different incentive effect and economic benefit of low carbon technology innovation. Through the comparative analysis, environmental policy tools in more advanced market mechanism have a better effect in promote the enterprise to choose low carbon technology innovation, and encouraging oriented environmental policy tools can promote the economic benefits of enterprise innovation activities. The results of this paper can provide a theoretical guide for the government to develop environmental policy tools