Abstract: The dynamic flux chamber and high time resolution technique (RA-915+ automatic mercury analyzer) were applied in this study to screen the mercury exchanging flux in  situ at the interface of sediment / atmosphere in the fluctuation zone when the water level of Three Gorges Reservoir was low. At the same time, the influencing factors were  analyzed. The results showed that the mercury exchanging flux was from -6.80±12.35 ng/(m2·h) to 28.17±36.17 ng/(m2·h). In the sunny days, mercury exchange flux showed the  same trend, the flux increased gradually from the early morning to the noon and the peak was appeared at noon, then, decreased gradually. But the trend was not obvious in the  cloudy days. In the warm season, mercury released from the sediment to the atmosphere in the daytime, the mercury exchanging flux showed a significant positive correlation with  air temperature, sediment temperature and light intensity and had a negative correlation with the relative humidity. While in the cold season, mercury deposited from atmosphere  to sediment in the daytime. Whether it was sunny or cloudy, there was a negative correlation between atmospheric mercury concentration and mercury exchanging flux at the  interface of sediment/atmosphere. During the daytime, light intensity and atmospheric mercury concentration were the major factors affecting the mercury exchange flux at the  sediment / atmosphere interface, while at night, the sediment temperature and atmospheric mercury concentration were the major influencing factors.