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Peatlands, with high spatial variability in ecotypes and microforms, constitute a significant part of the boreal landscape and play an important role in the global carbon (C) cycle. However, the effects of this peatland heterogeneity within the boreal landscape are rarely quantified. Here, we use field-based measurements, high-resolution land cover classification, and biogeochemical and atmospheric models to estimate the atmosphere-ecosystem C fluxes and corresponding radiative effect (RE) for a boreal landscape (Kaamanen) in northern Finland. Our result shows that the Kaamanen catchment currently functioned as a sink of carbon dioxide (CO2) and a source of methane (CH4). Peatlands (26% of the area) contributed 22% of the total CO2 uptake and 89% of CH4 emissions; forests (61%) accounted for 78% of CO2 uptake and offset 6% of CH4 emissions; water bodies (13%) offset 7% of CO2 uptake and contributed 11% of CH4 emissions. The heterogeneity of peatlands accounted for 11%, 88%, and 75% of the area-weighted variability (deviation from the area-weighted mean among different land cover types (LCTs) within the catchment) in CO2 flux, CH4 flux, and the combined RE of CO2 and CH4 exchanges over the 25-yr time horizon, respectively. Aggregating peatland LCTs or misclassifying them as non-peatland LCTs can significantly (p < 0.05) bias the regional CH4 exchange and RE estimates, while differentiating between drier non-inundated and wetter inundated peatlands can effectively reduce the bias. Current land cover products lack such details in peatland heterogeneity, which would be needed to better constrain boreal C budgets and global C-climate feedbacks.