Northern peatlands are key carbon reservoirs and natural sources of methane. The northern peatland soils have various mechanisms controlling water, energy and carbon cycles (soil freeze-thaw) which further make modeling the emissions a challenge. In this study, we developed the CoupModel with respect to more comprehensive representation of gas processes in soil and plants, and used it to simulate O2, CO2, CH4 as well as energy and water fluxes in three pristine northern peatlands across the thawing gradient (seasonal frost – degraded permafrost – continuous permafrost). These sites have 10-15 years of CO2 flux and CH4 flux measurement data. CoupModel reproduced the measured hourly CH4 fluxes with R2 (coefficient of determination) values of 0.60±0.02, 0.32±0.02 and 0.18±0.005 in Degerö Stormyr, Stordalen and Zackenberg, respectively. Our model simulation showed CH4 emissions from three sites along the Boreal-Arctic gradient have diverse sensitivities to temperature and WTD. Higher temperature sensitivity of CH4 was found in continuous permafrost zone (Zackenberg), and a turning point for WTD (-0.15~-0.1 m) found over three sites. Hysteresis exists in CH4 fluxes responding to water table, temperature and freezing-thawing cycles. We conclude that the newly developed CoupModel can adequately simulate the CH4 emission and its controls for northern peatlands. Our study revealed the response trajectories of peatland ecosystems across the permafrost region to environmental controls and highlighted the need for future peatland models to better simulate and predict the future CH4 dynamics in a changing climate.