Natural wetlands are the primary sources of CH4 emissions in the natural environment. However, the understanding of CH4 fluxes in floodplain wetlands remains limited. This study employed eddy covariance methods to observe CH4 fluxes over a three-year period in a subtropical wetland floodplain, specifically the Miscanthus sacchariflorus (M. sacchariflorus) ecosystem in Dongting Lake wetland. Our analysis focused on exploring the impact of flooding frequency on CH4 emissions, flood stimulation effect, time-lag effects, and the environmental factors influencing CH4 fluxes. The M. sacchariflorus ecosystem exhibited an annual CH4 emission rate of 14.54 g CH4C m−2 y−1. During the flood period, the average daily CH4 emissions reached 0.155 g CH4C m−2 d−1, contrasting with the pre-flood period's average of 0.014 g CH4C m−2 d−1. Moreover, the time-lag effect of flooding on CH4 emissions was found to be 10 days, representing the period between inundation and a substantial increase in CH4 emissions. Comparatively, in 2021, following three fluctuations in floodwaters, the average CH4 emission intensity during the flood period decreased by 46.2% and 48.9% when compared to the years 2019 and 2020 which both following one fluctuation, respectively. CH4 emissions during flooding are predominantly influenced by water depth (WD), wherein shallow WD corresponds to higher CH4 emissions. This correlation can be attributed to factors such as vegetation type, water-column pressure, and soil oxygen content. Therefore, increasing frequency of inundation and a higher WD hold promise as effective measures for mitigating CH4 emissions in floodplain wetlands.