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Abstract Methane (CH 4 ) emissions from tropical wetlands contribute 60%–80% of global natural wetland CH 4 emissions. Decreased wetland CH 4 emissions can act as a negative feedback mechanism for future climate warming and vice versa. The impact of the El Niño–Southern Oscillation (ENSO) on CH 4 emissions from wetlands remains poorly quantified at both regional and global scales, and El Niño events are expected to become more severe based on climate models’ projections. We use a process‐based model of global wetland CH 4 emissions to investigate the impacts of the ENSO on CH 4 emissions in tropical wetlands for the period from 1950 to 2012. The results show that CH 4 emissions from tropical wetlands respond strongly to repeated ENSO events, with negative anomalies occurring during El Niño periods and with positive anomalies occurring during La Niña periods. An approximately 8‐month time lag was detected between tropical wetland CH 4 emissions and ENSO events, which was caused by the combined time lag effects of ENSO events on precipitation and temperature over tropical wetlands. The ENSO can explain 49% of interannual variations for tropical wetland CH 4 emissions. Furthermore, relative to neutral years, changes in temperature have much stronger effects on tropical wetland CH 4 emissions than the changes in precipitation during ENSO periods. The occurrence of several El Niño events contributed to a lower decadal mean growth rate in atmospheric CH 4 concentrations throughout the 1980s and 1990s and to stable atmospheric CH 4 concentrations from 1999 to 2006, resulting in negative feedback to global warming.