<p>In the High Arctic and maritime Antarctic, sea animal guano deposition and repetitive freeze-thaw cycles (FTCs) strongly affect tundra soil carbon and nitrogen dynamics, thereby influencing greenhouse gas (GHG) emissions. However, their combined effects on GHG emissions remain understudied. Soil samples were collected from sea animal colonies (SACS) and non-SACS, including seabird colonies and normal tundra in the High Arctic, penguin/seal colonies and normal upland tundra in the maritime Antarctic, and incubated to investigate their combined effects on CH₄, CO₂ and N₂O emissions. CH₄ and N₂O emissions from almost all tundra soils were higher at a freezing temperature of -20 ℃ compared to -10 ℃ during FTCs. Extremely high cumulative CH₄ and CO₂ emissions occurred in penguin colony soils, whereas seal colony soils showed the highest N₂O emissions during FTCs. During the five consecutive FTCs, CO₂ and N₂O emissions from non-SACS gradually decreased with the number of FTCs, whereas penguin colony soils maintained high and stable CO₂, CH₄ or N₂O emissions, due to the rich nutrients and substrates derived from penguin guano input. Extra water addition reduced tundra soil CO₂ emissions during FTCs, but had no significant effects on CH₄ emissions, whereas 5–10 mL of water addition resulted in the highest N₂O emissions. N₂O emissions demonstrated significant positive correlation (<i>p</i> &lt; 0.05) with soil NH₄⁺-N and NO₃⁻-N contents during FTCs, closely associated with guano deposition. Our results underscored that the combination of sea animal guano deposition and freeze-thaw conditions greatly enhanced tundra soil GHG emissions, particularly in maritime Antarctic.</p>