Wetland loss and climate change are known to alter regional and global methane (CH<sub>4</sub>) budgets. Over the last six decades, an extensive area of marshland has been converted to cropland on the Sanjiang Plain in northeast China, and a significant increase in air temperature has also been observed there, while the impacts on regional CH<sub>4</sub> budgets remain uncertain. Through model simulation, we estimated the changes in CH<sub>4</sub> emissions associated with the conversion of marshland to cropland and climate change in this area. Model simulations indicated a significant reduction of 1.1 Tg yr<sup>−1</sup> (0.7–1.8 Tg yr<sup>−1</sup>) from the 1950s to the 2000s in regional CH<sub>4</sub> emissions. The cumulative reduction of CH<sub>4</sub> from 1960 to 2009 was estimated to be ~36 Tg (24–57 Tg) relative to the 1950s, and marshland conversion and the climate contributed 86% and 14% of this change, respectively. Interannual variation in precipitation (linear trend with <I>P</I> > 0.2) contributed to yearly fluctuations in CH<sub>4</sub> emissions, but the relatively lower amount of precipitation over the period 1960–2009 (47 mm yr<sup>−1</sup> lower on average than in the 1950s) contributed ~91% of the reduction in the area-weighted CH<sub>4</sub> flux. Global warming at a rate of 0.3 ° per decade (<I>P</I> < 0.001) has increased CH<sub>4</sub> emissions significantly since the 1990s. Relative to the mean of the 1950s, the warming-induced increase in the CH<sub>4</sub> flux has averaged 19 kg ha<sup>−1</sup> yr<sup>−1</sup> over the last two decades. In the RCP (Representative Concentration Pathway) 2.6, RCP 4.5, RCP 6.0 and RCP 8.5 scenarios of the fifth IPCC assessment report (AR5), the CH<sub>4</sub> fluxes are predicted to increase by 36%, 52%, 78% and 95%, respectively, by the 2080s compared to 1961–1990 in response to climate warming and wetting.