Cooperating in low-carbon linkage development is an inevitable choice for manufacturing and logistics enterprises in emerging economies and government plays an important role in the cooperation. This paper constructs a three-party evolutionary game theory model to study the behavior of the government, manufacturing, and logistics enterprises in such cooperation. Based on the game income matrix of strategy combinations, replicated dynamic equations are established and used to investigate the equilibrium state of the game; the local stability of the equilibrium state in various scenarios is analyzed using Jacobian matrix and stability theory, 3 D spatial replicated phase diagrams are used to show the strategy choice trends of participants. This paper also summarises the rules of game behavior under different income parameters. We found that additional developmental cost in low-carbon linkage is a key factors that directly affects the game results, and government plays an important role in the development: in the early stage of development when the investment is high, the government can promote cooperation by regulations or financial incentives. The findings are corroborated in numerical simulations. This paper enriches the literature on factors that affect decision-making in low-carbon linkage development, and provides useful insights to improve government intervention to promote a low-carbon economy.