Methane (CH₄) emissions from tropical wetlands contribute 60%–80% of global natural wetland CH₄ emissions. Decreased wetland CH₄ 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 CH₄ 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 CH₄ emissions to investigate the impacts of the ENSO on CH₄ emissions in tropical wetlands for the period from 1950 to 2012. The results show that CH₄ 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 CH₄ 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 CH₄ emissions. Furthermore, relative to neutral years, changes in temperature have much stronger effects on tropical wetland CH₄ 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 CH₄ concentrations throughout the 1980s and 1990s and to stable atmospheric CH₄ concentrations from 1999 to 2006, resulting in negative feedback to global warming.