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• The annual CH 4 emission of the Miscanthus sacchariflorus ecosystem was 14.54 g CH 4 C m−2 y−1. • The effect of flood stimulation on CH 4 emissions ranged from 0.054 to 0.177 g CH 4 C m−2 d−1. • The time-lag effect of flooding on CH 4 emissions was observed to be approximately 10 days. • A higher frequency of inundation demonstrated a significant reduction in CH 4 emissions by approximately 46.2–48.9%. Natural wetlands are the primary sources of CH 4 emissions in the natural environment. However, the understanding of CH 4 fluxes in floodplain wetlands remains limited. This study employed eddy covariance methods to observe CH 4 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 CH 4 emissions, flood stimulation effect, time-lag effects, and the environmental factors influencing CH 4 fluxes. The M. sacchariflorus ecosystem exhibited an annual CH 4 emission rate of 14.54 g CH 4 C m−2 y−1. During the flood period, the average daily CH 4 emissions reached 0.155 g CH 4 C m−2 d−1, contrasting with the pre-flood period's average of 0.014 g CH 4 C m−2 d−1. Moreover, the time-lag effect of flooding on CH 4 emissions was found to be 10 days, representing the period between inundation and a substantial increase in CH 4 emissions. Comparatively, in 2021, following three fluctuations in floodwaters, the average CH 4 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. CH 4 emissions during flooding are predominantly influenced by water depth (WD), wherein shallow WD corresponds to higher CH 4 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 CH 4 emissions in floodplain wetlands. [ABSTRACT FROM AUTHOR]