To investigate the transport of mercury from glacier to runoff in typical inland glacial area in the Tibetan Plateau, we selected Zhadang glacier and Qugaqie river Basin located in the Nyainqentanglha Range region and collected samples from snow pit, glacier melt-water and Qugaqie river water during 15~(th) August to 9~(th) September 2011. Mercury speciation and concentrations were determined and their distribution and controlling factors in different environmental compartments were analyzed. The results showed that the average THg concentrations were (3.795.12) ng·L~(-1),(1.060.77) ng·L~(-1)and (1.020.24) ng·L~(-1) for glacier snow, glacier melt-water and Qugaqie river water, respectively, all of which were at the global background levels. Particulate-bound mercury accounted for large proportion of mercury in all environmental matrices, while mercury in glacial melt-water was controlled by total suspended particle, and mercury in Qugaqie river water co-varied with runoff. With the increase of temperature, glacier melted and released water as well as mercury into glacier-fed river. Total mercury concentrations in glacier melt water, upstream and downstream peaked at 14:00, 16:00 and after 20:00, respectively, reflecting the process of mercury release from glacier and its subsequent transport in the glacier fed river. The transport of riverine mercury was controlled by multiple factors. Under the context of climate change, glacier ablation and the increasing runoff will play increasingly important roles in mercury release and transport.