Abstract: With the aid of the eddy covariance technique, monitoring was carried out of net ecosystem CO₂ exchange (NEE) of the Nanji Wetland National Nature Reserve, sitting in the south of Poyang Lake, for analysis of diurnal variation of NEE and its affecting factors, during non-flooding and flooding periods of April, 2015-October, 2016. Results show that during the non-flooding period, diurnal variation of NEE exhibited a typical "U" shaped curve. In the day, CO₂ uptake peaked up to 18.24 μmol·m^-2·s^-1, while at the night CO₂ release did up to 24.92 μmol·m^-2·s^-1. During the flooding period, the vegetation in the area was submerged by water, except for the parts in shoals and high lands around the lake. Diurnal variation of NEE in this period didn't have any distinct characteristics, and was much narrower in amplitude than that in the non-flooding period. In daytime, CO₂ uptake peaked up to 2.29 μmol·m^-2·s^-1 while at night CO₂ release did up to 12.66 μmol·m^-2·s^-1. Correlation analysis and principal component analysis show that during the non-flooding period, monthly mean daily NEE variation in daytime was the most closely related to photosynthetic photon quanta flux density, and then to air temperature, precipitation, soil moisture content and soil temperature, whereas at night, it was closely related to air temperature, soil temperature and soil moisture content. During the flooding period, monthly mean daily NEE variation in daytime was related to photosynthetic photon quanta flux density and soil moisture content, whereas at night, it was related to soil temperature, soil moisture content and air temperature.