An increase of greenhouse gases content (СО2, CH4, N2O and others) in the Earth’s atmosphere affects radiation balance leading to the climate changes of the planet. Anthropogenic CO2 emissions from the territory of megacities play an important role in this process contributing approximately 70% of the total anthropogenic emissions of carbon dioxide. In this study integral anthropogenic CO2 emissions of Saint-Petersburg megacity were estimated using observation data of EMME 2019 campaign. Here we used a new approach of inverse problem solution which was based on a priori data and scale coefficients applied only to the city’s areas covered by observations. New estimates of the integral anthropogenic CO2 emissions of Saint-Petersburg are in a range 52–72 MtCO2/year. These emissions are significantly higher than inventory-based estimates (~30 MtCO2/year). However, the minimal value of this range (52 MtCO2/year) is lower by approximately 21% than emissions which were found by us earlier using EMME 2019 data (65 MtCO2/year).