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Northern Eurasia is one of the largest terrestrial carbon reservoirs on the Earth's surface. However, since the coverage of surface CO₂ observations is still limited, the response to the climate variability remains uncertain. We estimated monthly CO₂ fluxes for three sub-regions in Northern Eurasia (north of ~60°N), Northeastern Europe, Western Siberia and Eastern Siberia, using CO₂ retrievals from the Japanese Greenhouse Gases Observing SATellite (GOSAT). The variations of estimated CO₂ fluxes were examined in terms of the regional climate variability, for the three consecutive growing seasons of 2009–2011. The CO₂ fluxes estimated using GOSAT data are highly correlated with the surface temperature anomalies in July and August (r > 0.8) while no correlation is found in the CO₂ fluxes estimated only using surface observations. The estimated fluxes from GOSAT data exhibit high negative correlations with one-month lagged positive precipitation anomalies in late summer (r > −0.7) through surface temperature and the Normalized Difference Vegetation Index (NDVI). The results indicate that GOSAT data reflects the changes in terrestrial biospheric processes responding to climate anomalies. In 2010, a large part of Eurasia experienced an extremely hot and dry summer, while cold and wet weather conditions were recorded in Western Siberia. The CO₂ fluxes estimated from GOSAT data showed a reduction of net CO₂ uptake in Northeastern Europe and Eastern Siberia, but the enhancement of net CO₂ uptake in Western Siberia. These opposite sub-regional flux anomalies can be explained by the different climate anomalies on a sub-regional scale in Northern Eurasia. Thus, this study demonstrates that space-based observations by GOSAT compensate for the lack of ground-based observational coverage so as to better capture the inter-annually varying atmosphere-terrestrial biosphere CO₂ exchange on a regional scale.