This study investigated the seasonal and daily variations of the total gaseous mercury (TGM) concentration in the ambient atmosphere, the correlation of TGM concentration with meteorological parameters (e.g., temperature, humidity, and wind speed) and criteria air pollutant concentrations (e.g., SO2, NOx, CO, O3, PM10, and PM2.5), as well as the transportation routes, at the Penghu Islands. The field measurement results showed that the average TGM concentration during the monitoring period was 3.17 ± 1.17 ng/m3, within the range of 1.17–8.63 ng/m3, with the highest concentration being observed in spring, while the TGM concentration typically increased in the morning, reached its peak concentration, and then started to decrease at nightfall. Moreover, the lowest average TGM concentration of 1.81 ± 0.15 ng/m3 was observed in summer, and this figure is close to the background TGM concentration of the Northern Hemisphere (1.6–1.8 ng/m3). The correlation analysis indicated that TGM concentration correlated positively with SO2, NOx, CO, O3, PM10, and PM2.5 and negatively with ambient temperature, relative humidity, and wind speed. In addition, the transportation route analysis showed that elevated TGM concentrations could be transported from either North China, East China, or South China to the Penghu Islands, while those originating from the South China Sea had the lowest contribution to the TGM levels at the Penghu Islands. Therefore, local sources and open burning might be mainly influenced by the long-range transportation of air masses, as the prevailing wind direction and air mass transportation routes potentially play critical roles in the variation of TGM concentration at the Penghu Islands.