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Abstract The Chukchi Sea is an increasing CO₂sink driven by rapid climate changes. Understanding the seasonal variation of air‐sea CO₂exchange and the underlying mechanisms of biogeochemical dynamics is important for predicting impacts of climate change on and feedbacks by the ocean. Here, we present a unique data set of underway sea surface partial pressure of CO₂(pCO₂) and discrete samples of biogeochemical properties collected in five consecutive cruises in 2014 and examine the seasonal variations in air‐sea CO₂flux and net community production (NCP). We found that thermal and non‐thermal effects have different impacts on sea surfacepCO₂and thus the air‐sea CO₂flux in different water masses. The Bering summer water combined with meltwater has a significantly greater atmospheric CO₂uptake potential than that of the Alaskan Coastal Water in the southern Chukchi Sea in summer, due to stronger biological CO₂removal and a weaker thermal effect. By analyzing the seasonal drawdown of dissolved inorganic carbon (DIC) and nutrients, we found that DIC‐based NCP was higher than nitrate‐based NCP by 66%–84% and attributable to partially decoupled C and N uptake because of a variable phytoplankton stoichiometry. A box model with a non‐Redfield C:N uptake ratio can adequately reproduce observedpCO₂and DIC, which reveals that, during the intensive growing season (late spring to early summer), 30%–46% CO₂uptake in the Chukchi Sea was supported by a flexible stoichiometry of phytoplankton. These findings have important ramification for forecasting the responses of CO₂uptake of the Chukchi ecosystem to climate change.