Due to promote manufacturing enterprises to carry out green technology innovation practice smoothly, achieve the goal of energy conservation and emission reduction, and win green competitive advantage, this paper first divides the green technology innovation path into two types, namely internal independent R&D of green technology (IIGT) and external green technology introduction (EGTI), and analyzes the operation mechanism of these two types of paths. Secondly, a two-agent game model of different types of environmental regulation tools on the choice of green technology innovation path of manufacturing enterprises is constructed. To be sure, the manufacturing enterprises include the leader enterprise A and the follower enterprise B. It is assumed that the two groups of manufacturing enterprises produce the same products or provide the same services in the natural state without considering other influencing factors. Finally, stability analysis and numerical simulation are employed to compare and analyze the heterogeneous effects of different environmental regulation tools on the path selection of green technology innovation in manufacturing enterprises.The simulation shows that when the government adopts or does not adopt environmental regulation means, the system, leader enterprise A and follower enterprise B will eventually choose the path of IIGT or EGTI respectively after a long-term evolution process. However, the effects of subsidy for green technology innovation and carbon tax rate on the path selection of green technology innovation are different among the three parties. Specifically, when the government adopts the means of subsidy for green technology innovation, the leader enterprise A will actively choose the the path of IIGT earlier than the follower enterprise B. On the contrary, when the government adopts the means of carbon tax, the leader enterprise A will actively choose the the path of IIGT later than the follower enterprise B. The research of this paper is helpful to explore the green and sustainable development mode of China's manufacturing industry under the dual constraints of environment and resources, and provides decision support for the relevant national departments to make relevant policies.