Cities occupy only 3% of the earth's land area, yet they contribute over 70% of anthropogenic CO2 emissions. Accurately quantifying the corresponding uncertainty of CO2 emissions at the city scale is the first step in simulating global/regional greenhouse gas concentration and implementing effective emission reduction policies. As the world's largest emitter, China has committed to reaching its CO2 emissions peak by 2030, and cities are facing substantial pressure to reduce CO2 emissions. The Yangtze River Delta (YRD) region is treated as the largest urban agglomeration in China and globally. Despite the availability of multiple emission inventories, comprehensive assessments of city-level CO2 emissions uncertainty within this region are still lacking. This study focused on the YRD region, compared six inventories and used nighttime light intensity, GDP, population, and satellite-based xCO2 concentrations as proxy data to identify potential sources of emission bias. The findings are as follows: (1) The city-level CO2 emissions in the YRD region ranged from tens of Mt to approximately 600 Mt. From 2010 to 2019, emissions in the region increased slowly. However, emission intensity (calculated by dividing the CO2 emissions by the Gross Domestic Product) showed a declining trend. The relatively low proportion of point source emissions in EDGAR inventory is attributed to its reliance on the point source CARMA, which overlooks smaller point sources. (2) The average uncertainties for low emission (0–50 Mt), medium emission (50–100 Mt) and high emission (>100 Mt) cities were 51.1%, 34.0%, and 45.0%, respectively. The absolute errors of emissions showed strong positive correlations with proxy data. There exists a logarithmic relationship between them and uncertainty, which can assist in estimating emission uncertainty in other cities in the future. (3) The ratios of biological CO2 flux to the ten-year average of CO2 emissions varied between-6.79% and −0.02%, which are much smaller than the uncertainty of anthropogenic emissions, the comparisons indicate that recent large biases in estimating anthropogenic CO2 emissions hinder the evaluation of carbon neutrality ability.