“Net-zero carbon emissions” is a critical policy for the government in Taiwan aimed at mitigating greenhouse gas effects caused by CO2 emissions. The promotion of green transportation is a strategic approach to reducing this greenhouse effect, attracting interest from public and private sectors as well as researchers. Metro and rail transportation systems are key components of green transportation, effectively drawing users away from private cars and significantly reducing greenhouse gas emissions. However, these systems heavily rely on electricity for both train operations and station services, resulting in CO2 emissions through electricity consumption. This paper proposes a two-stage network directional distance function (DDF) model to measure the efficiencies of environment, energy, and CO2 emissions in metro systems. Empirical analyses were conducted using input-output data from the Taipei Rapid Transit Corporation (TRTC) and the Kaohsiung Rapid Transit Corporation (KRTC). A case study of the Taipei MRT indicates a need to decrease electricity consumption by 4.02% and CO2 emissions by 2.99% during production. In contrast, the Kaohsiung MRT demonstrates higher efficiency in both energy and emissions. Additionally, both metro systems should aim to reduce energy consumption in the service stage by 0.58% for Taipei and 1.44% for Kaohsiung, while CO2 emissions reductions of 7.66% and 0.82% are recommended, respectively. The proposed model offers operators valuable insights into environmental, energy, and CO2 emission efficiencies for both production and service stages, enhancing the understanding of “energy saving and carbon reduction” strategies beyond traditional one-stage performance evaluations.