Methane (CH4) emissions from the drawdown area of the Three Gorges Reservoir (TGR) have not been thoroughly investigated even though the drawdown area encompasses one third of the reservoir surface. In this study, CH4 emissions from different land uses were measured in the TGR drawdown area. The average diffusive CH4 emissions were 2.61, 0.19, 0.18, and 0.12 mg CH4 m−2 h−1 in rice paddies, fallow lands, deforested lands, and croplands, respectively, and were positively related to the duration of the inundated season among the latter three land uses. On average the drawdown areas studied here (except rice paddies) were sources in the inundated season (0.22 ± 0.26 mg CH4 m−2 h−1) and a sink in the drained season (−0.008 ± 0.035 mg CH4 m−2 h−1). The water level was the dominant factor that controlled whether the drawdown area was either inundated or drained, which in turn determined whether the drawdown area was a source or sink of CH4 emissions. The average diffusive CH4 emissions from the fallow lands, croplands, and deforested lands increased as the distance from the dam increased from Zigui (0.10 ± 0.15 mg CH4 m−2 h−1) to Wushan (0.15 ± 0.29 mg CH4 m−2 h−1) to Yunyang (0.24 ± 0.27 mg CH4 m−2 h−1), which could reflect different sediment characteristics and water velocities. The total CH4 emission from the drawdown area was estimated to range from 1033.5 to 1333.9 Mg CH4 yr−1, which would account for 42–54% of the total CH4 emissions from the water surface of TGR.