Reducing anthropogenic fossil fuel CO₂ (FFCO₂) emissions in urban areas is key to mitigating climate change. To better understand the spatial characteristics and temporal variations in urban CO₂ levels in the Beijing (BJ) region, we conducted a long-term CO₂ simulation study by using the Weather Research and Forecasting WRF-Chem model and CO₂ observation data. To assess the model performance, three representative sites with high-precision CO₂ observation data were chosen in this study: the rural regional background Shangdianzi (SDZ) site, the suburban Xianghe (XH) site, and the urban BJ site. The simulation results generally captured the observed variations at these three sites, but the model performed much better at the SDZ and XH sites, with mean biases of −0.7 ppm and −2.3 ppm, respectively, and RMSE of 12.3 ppm and 21.4 ppm, respectively. The diurnal variations in the model results agreed well with those in the observed CO₂ concentrations at the SDZ and XH sites during all seasons. In the meanwhile, the diurnal variations in the modeled FFCO₂ were similar to those in the CO₂ observation with a positive bias at the BJ site, which may have been caused by higher emissions especially in winter. Moreover, both the modeled FFCO₂ and biospheric CO₂ (BIOCO₂) have positive correlations with the observed CO₂ concentration, whereas the planetary boundary layer height (PBLH) and observed CO₂ concentration exhibited negative correlations at all sites. In addition, the contributions of FFCO₂ and BIOCO₂ to CO₂ varies depending on the seasons and the location of sites.