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The atmosphere‐land‐ocean fluxes of CO₂ were derived for 64 partitioned areas of the globe (22 over the ocean and 42 over the land) using a time‐dependent inverse (TDI) model for the period of January 1988 to December 2001. The model calculation partially follow the TransCom‐3 protocol, and is constrained by atmospheric CO₂ concentration data from 87 stations and fully time‐dependent atmospheric transport model simulations. The air‐to‐land and air‐to‐sea fluxes averaged over the 1990s are estimated at 1.15 ± 0.74 and 1.88 ± 0.53 Pg‐C yr⁻¹, respectively. These estimates, however, remain uncertain owing to sampling biases arising from the sparse distribution of atmospheric CO₂ data, are compared with other estimates by various methods. The sensitivity analysis indicates that the differences in fluxes and flux variability caused by the choices of initial conditions for the TDI model are smaller …