Three heights (180 m, 175 m and 155 m) located in a typical drawdown area in Wangjiagou of the Three Gorges Reservoir were selected for studying the N2O emissions from subtropical reservoirs. The experimental period lasted two years from August 2010 to August 2012. The methods of static opaque chambers during the drainage period and floating chambers during flooding period were adopted in this study. The heights of 175 m and 155 m were both located in the drawdown area, whereas the 180 m height was located in the land as a control to 175 m and 155 m. N2O fluxes showed clear seasonal trends at each height and remarkable differences were observed between the two years at the 180 m height. N2O fluxes were lowest in spring at the 180 m height. N2O fluxes showed a single-peak pattern with climax in summer in the first year, whereas a double-peak pattern with climax in summer and after dry-wet alternating in the next year after the highest water level of 175 m was succeeded in the Three Gorges Reservoir. N2O fluxes presented a single-peak shape with summer climax at the 155 m height. Additionally, N2O fluxes were higher during the drainage period than in the flooding period at both the 175 m and 155 m heights. The order of the annual N2O cumulative emissions at the three heights was 175 m (853.92 mg·m-2) > 180 m (336.69 mg·m-2) > 155 m (324.69 mg·m-2), and there was a notable difference between 175 m and 155 m, indicating that short-term flooding could increase N2O emissions but long-term flooding could restrain N2O emissions. Correlation analysis showed that there were no obvious relativities between N2O fluxes and environmental factors in the land and during the drainage period. However, N2O fluxes were significantly negatively correlated with water temperature and wind speed during the flooding period. Principal component analysis found that soil nutrient conditions and physicochemical properties were the most important factors for N2O emissions in the land, the nitrogen distribution in water was a main determinant for N2O emissions during the flooding period, and soil physicochemical properties and microbial activity importantly affected N2O emissions during the drainage period in the drawdown area.