In this study, we examined the structure of an ensemble-based coupled atmosphere-chemistry forecast error covariance. The Weather Research and Forecasting (WRF) model coupled with Chemistry (WRF-Chem), a coupled atmosphere-chemistry model, was used to create an ensemble error covariance. The control variable includes both the dynamical and chemistry model variables. A synthetic single observation experiment was designed in order to evaluate the cross-variable components of a coupled error covariance. The results indicate that the coupled error covariance has important cross-variable components that allow a physically meaningful adjustment of all control variables. The additional benefit of the coupled error covariance is that a cross-component impact is allowed; e.g., atmospheric observations can exert an impact on chemistry analysis, and vice versa. Given the realistic structure of ensemble forecast error covariance produced by the WRF-Chem, we anticipate that the ensemble-based coupled atmosphere-chemistry data assimilation will respond similarly to assimilation of real observations.