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Ponds are abundant in the boreal peatland landscape, which are potential hotspots for greenhouse gas (GHG) emissions. However, compared to large lakes, ponds are difficult to identify by satellite, and they have not been adequately studied. Here, we observed methane (CH₄), carbon dioxide (CO₂), and nitrous oxide (N₂O) fluxes in the growing season at three sites along the water table gradient from the pelagic zone, littoral zone and bog across a shallow pond in a boreal peatland landscape in Northeastern China. The results showed that the littoral zone, dominated by herb Carex, was the hotspot for CH₄ emissions. CH₄ fluxes in littoral zone averaged 78.98 ± 19.00 mg m⁻² h⁻¹. The adjacent bog was a weak source of CH₄ emissions, with an average flux of 0.07 ± 0.05 mg m⁻² h⁻¹. Within the pond, CH₄ was mainly emitted through ebullition, accounting for 88.56% of the total CH₄ fluxes, and the ebullition fluxes were negatively correlated with dissolved oxygen (DO). CO₂ fluxes were highest in the pelagic zone, with an average of 419.76 ± 47.25 mg m⁻² h⁻¹. Wind and strong sediment respiration were key factors that led to the high fluxes. The observed three sites were all atmospheric N₂O sinks ranging from −0.92 to −10.90 μg m⁻² h⁻¹. This study highlights the spatial variation in greenhouse gas fluxes from the pond and its adjacent bog, ignoring the ecotone area may underestimate CH₄ fluxes. Although ponds are a hotspot for CH₄ and CO₂ emissions, they can also be a sink for N₂O, which provides a reference for the quantification of global pond GHG fluxes. Therefore, finer-scale in situ observations are necessary to better understand the feedback of permafrost peatland ponds to global warming.