Northern peatlands are a major natural source of methane (CH4) to the atmosphere. Permafrost conditions and spatial heterogeneity are two of the major challenges for estimating CH4 fluxes from the northern high latitudes. This study reports the development of a new model to upscale CH4 fluxes from plant communities to ecosystem scale in permafrost peatlands by integrating an existing biogeochemical model DeNitrification-DeComposition (DNDC) with a permafrost model Northern Ecosystem Soil Temperature (NEST). A new ebullition module was developed to track the changes of bubble volumes in the soil profile based on the ideal gas law and Henry’s law. The integrated model was tested against observations of CH4 fluxes measured by closed chambers and eddy covariance (EC) method in a polygonal permafrost area in the Lena River Delta, Russia. Results from the tests showed that the simulated soil temperature, summer thaw depths and CH4 fluxes were in agreement with the measurements at the five chamber observation sites; and the modeled area-weighted average CH4 fluxes were similar to the EC observations in seasonal patterns and annual totals although discrepancy existed in shorter time scales. This study indicates that the integrated model, NEST–DNDC, is capable of upscaling CH4 fluxes from plant communities to larger spatial scales.