Decadal trends and interannual variations in the hydroxyl radical (OH), while poorly constrained at present, are critical for understanding the observed evolution of atmospheric methane (CH4). Through analyzing the OH fields simulated by the model ensemble of the Chemistry–Climate Model Initiative (CCMI), we find (1) the negative OH anomalies during the El Niño years mainly corresponding to the enhanced carbon monoxide (CO) emissions from biomass burning and (2) a positive OH trend during 1980–2010 dominated by the elevated primary production and the reduced loss of OH due to decreasing CO after 2000. Both two-box model inversions and variational 4D inversions suggest that ignoring the negative anomaly of OH during the El Niño years leads to a large overestimation of the increase in global CH4 emissions by up to 10 ± 3 Tg yr−1 to match the observed CH4 increase over these years. Not accounting for the increasing OH trends given by the CCMI models leads to an underestimation of the CH4 emission increase by 23 ± 9 Tg yr−1 from 1986 to 2010. The variational-inversion-estimated CH4 emissions show that the tropical regions contribute most to the uncertainties related to OH. This study highlights the significant impact of climate and chemical feedbacks related to OH on the top-down estimates of the global CH4 budget.