The Southern Ocean strongly modulates the global ocean carbon sinks, yet biases in air–sea CO₂ flux remain pervasive over the generation of models. Due to the spatially diverse characteristics of this region, we focus on the Antarctic Circumpolar Current upwelling zone, a weak net CO₂ sink with marked spatial and seasonal variability and localized CO₂ outgassing. Here, seasonal physical and biogeochemical drivers exert opposing influences on surface pCO₂, challenging accurate simulation of air-sea CO₂ exchange. Using observation-based benchmarks, we elucidate the uncertainties of seasonal air-sea CO₂ fluxes (fgCO₂) in an ensemble of Earth system models, including the underlying thermal and non-thermal processes. The inter-model discrepancies are predominantly driven by biases in non-thermal contributions. Notably, some models reproduce the observed annual mean CO₂ fluxes through mutually compensating or amplifying seasonal thermal and non-thermal errors. Inter-model biases in the vertical dissolved inorganic carbon (DIC) gradient correlate strongly with the fgCO₂ errors (R = 0.80). Future improvements in simulating the observed physical and biogeochemical dynamics, particularly those regulating the seasonal upper-ocean DIC distribution, should be prioritized to further narrow global carbon sink uncertainty and improve future projections.