Commuters spend considerable time, in some cases up to 1–2 h a day, traveling in metro trains. However, few studies have compared air quality between trains traveling above-ground and underground. This study measures the PM10, PM2.5, particle number (PN) and CO2 levels inside metro trains traveling in underground tunnels and on elevated tracks on a metro line in the Taipei metro system. The results demonstrated that PM10, PM2.5 and CO2 levels inside metro trains traveling in underground environments are approximately 20–50% higher than those in above-ground environments. However, PN levels inside metro trains traveling in underground environments are approximately 20% lower than those in above-ground ones. These measurement results reveal that levels of pollutant species inside the metro trains are significantly affected by traveling environmental conditions––in underground tunnels or on elevated tracks. Moreover, the levels of pollutant species inside the metro trains traveling on the same route are also different in different traveling directions. Fine PM inside the metro trains is transferred from the outside and significantly influenced by the surrounding conditions of the trains. Additionally, a high fraction of large coarse PM (> 10 μm) is observed inside the metro trains, possibly due to re-suspension by the movement of commuters. The measurement results show that, unlike PM, which is transferred from outside environments, CO2 inside metro trains is elevated internally by exhalation from commuters. Clearly, CO2 exhaled by commuters could accumulate inside metro trains and, compared to PM, is not as easily removed by the ventilation system when air circulation does not provide enough fresh air in the metro trains, particularly in trains traveling in underground environments.