Nowadays, different approaches for CO2 anthropogenic emission estimation are applied to control agreements on greenhouse gas reduction. Some methods are based on the inverse modelling of emissions using various measurements and the results of numerical chemistry transport models (CTMs). Since the accuracy and precision of CTMs largely determine errors in the approaches for emission estimation, it is crucial to validate the performance of such models through observations. In the current study, the near‐surface CO2 mixing ratio simulated by the CTM Weather Research and Forecasting—Chemistry (WRF‐Chem) at a high spatial resolution (3 km) using three different sets of CO2 fluxes (anthropogenic + biogenic fluxes, time‐varying and constant anthropogenic emissions) and from Copernicus Atmosphere Monitoring Service (CAMS) datasets have been validated using in situ observations near the Saint Petersburg megacity (Russia) in March and April 2019. It was found that CAMS reanalysis data with a low spatial resolution (1.9 × 3.8°) can match the observations better than CAMS analysis data with a high resolution (0.15 × 0.15°). The CAMS analysis significantly overestimates the observed near‐surface CO2 mixing ratio in Peterhof in March and April 2019 (by more than 10 ppm). The best match for the CAMS reanalysis and observations was observed in March, when the wind was predominantly opposite to the Saint Petersburg urbanized area. In contrast, the CAMS analysis fits the observed trend of the mixing ratio variation in April better than the reanalysis with the wind directions from the Saint Petersburg urban zone. Generally, the WRF‐Chem predicts the observed temporal variations in the near-surface CO2 reasonably well (mean bias ≈ (−0.3) − (−0.9) ppm, RMSD ≈ 8.7 ppm, correlation coefficient ≈ 0.61 ± 0.04). The WRF‐Chem data where anthropogenic and biogenic fluxes were used match the observations a bit better than the WRF‐Chem data without biogenic fluxes. The diurnal time variation in the anthropogenic emissions influenced the WRF‐Chem data insignificantly. However, in general, the data of all three WRF‐Chem model runs give almost the same CO2 temporal variation in Peterhof in March and April 2019. This could be related to the late start of the growing season, which influences biogenic CO2 fluxes, inaccuracies in the estimation of the biogenic fluxes, and the simplified time variation pattern of the CO2 anthropogenic emissions.