The long tunnel is a fixed, semi-closed environment where excessive concentrations of air pollutants are easily accumulated. This can potentially have a serious affect on drivers' health, especially when operating vehicles in the long tunnel for a lengthy period of time. Therefore, studies on pollutant emission characteristics and influential factors of emission in the tunnel are important. In this study, several sampling sites were arranged in the 12.9 km long Hsueh-shan Tunnel, to help understand the piston effect of pollutant emission characteristics and spatial concentration distribution. In order to understand the influential factor of air quality in the long tunnel, several tests were run during a closed period, an open period, a non-rush hour period, and a rush hour period. The results showed that during the closed period, the CO, SO2, NOx, and PM10 concentrations in the Hsueh-shan Tunnel were in the range of: 0.58–0.64 ppm, 0.94–1.08 ppb, 6.33–7.11 ppb, and 45.4–54.3 μg/m3, respectively. In contrast, during the open period, the CO, SO2, NOx, and PM10 concentrations reached 12–39 ppm, 20–48 ppb, 1.2–3.1 ppm, and 75–177 μg/m3, respectively. In the Hsueh-shan Tunnel, the number of vehicles at rush hour was about 1400 per hour, three times higher than during non-rush hour. The piston effect is very obvious since pollutant concentrations are elevated with increasing distance from the inlet. This study found that the pollutant concentration near the outlet can be three times higher than that near the inlet.