We developed WRF-CO2 4D-Var, a carbon dioxide data assimilation system based on the online atmospheric chemistry–transport model WRF-Chem. The accuracy of the model for sensitivity calculation and inverse modeling is assessed with pseudo-observation data. In this system, carbon dioxide is treated as an atmospheric tracer and its influence on meteorology is ignored. This system provides a useful model tool for regional-scale carbon source attribution and uncertainty assessment.