After our previous study about methane (CH4) emissions from littoral marshes of the Three Gorges Reservoir (TGR), Chinese dams have raised a world-wide concern. Through measurements from the surface of the TGR, a CH4 emission rate was recorded as 0.26 ± 0.38 mg CH4 m−2 h−1 (Mean ± SD), relatively low compared with those from other hydropower reservoirs. We also recorded CH4 emission rate from the surface of downstream water, which was also relatively low (0.24 ± 0.37 mg CH4 m−2 h−1). Such result may indicate that TGR is not a great CH4 emitter (not “CH4 menace”). One possible reason for such a low emission rate is that measures to maintain water quality and protect environment and ecosystem decrease the input of organic materials (for methanogenesis), which in turn limits the CH4 production in the sediment of the TGR. We also found that CH4 emission from the flooding drawdown area (0.29 ± 0.37 mg CH4 m−2 h−1) was higher than other permanently flooded sites (0.23 ± 0.38 mg CH4 m−2 h−1). Because of annual vegetation re-growth, the drawdown zone is the especially important carbon source for methanogenesis in flooding season. Interestingly, we also observed that mean CH4 emission was significantly higher in winter than in spring and summer. This was partly due to seasonal dynamics of hydrology. In order to estimate the net CH4 emissions caused by the reservoir and reservoir operation, the best approach would be Life Cycle Analysis.