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Permafrost thawing may lead to the release of carbon and nitrogen in high-latitude regions of the Northern Hemisphere, mainly in the form of greenhouse gases. Our research aims to reveal the effects of permafrost thawing on CH4 and N2O emissions from peatlands in Xiaoxing’an Mountains, Northeast China. During four growing seasons (2011–2014), in situ CH4 and N2O emissions were monitored from peatland under permafrost no-thawing, mild-thawing, and severe-thawing conditions in the middle of the Xiaoxing’an Mountains by a static-chamber method. Average CH4 emissions in the severe-thawing site were 55-fold higher than those in the no-thawing site. The seasonal variation of CH4 emission became more aggravated with the intensification of permafrost thawing, in which the emission peaks became larger and the absorption decreased to zero. The increased CH4 emissions were caused by the expansion of the thawing layer and the subsequent increases in soil temperature, water table, and shifts of plant communities. However, N2O emissions did not change with thawing. Permafrost thawing increased CH4 emissions but did not impact N2O emissions in peatlands in the Xiaoxing’an Mountains. Increased CH4 emissions from peatlands in this region may amplify global warming.