Against the backdrop of low-carbon transportation and urban logistics transformation, metro-based freight is regarded as an important pathway for emission reduction. This paper constructs a tripartite evolutionary game model involving the government, logistics enterprises, and metro operators, and analyzes multi-agent strategy evolution and the influence of key parameters using replicator dynamics equations and numerical simulation. The results show that well-designed subsidies and penalties can effectively promote a stable state characterized by “active government intervention, active response from logistics enterprises, and low-carbon integrated passenger and freight transportation by metro operators”. Reducing the cost of transformation can improve evolutionary efficiency, while excessively high subsidies may weaken the government’s willingness to intervene. This study provides insights for optimizing low-carbon transportation policies and supporting the development of metro-based freight systems.