Abstract Background Quantifying CO2 emissions from cities is of great importance because cities contribute more than 70% of the global total CO2 emissions. As the largest urbanized megalopolis region in northern China, the Beijing-Tianjin-Hebei (Jing-Jin-Ji, JJJ) region (population: 112.7 million) is under considerable pressure to reduce carbon emissions. Despite the several emission inventories covering the JJJ region, a comprehensive evaluation of the CO2 emissions at the prefectural city scale in JJJ is still limited, and this information is crucial to implementing mitigation strategies. Results Here, we collected and analyzed 8 published emission inventories to assess the emissions and uncertainty at the JJJ city level. The results showed that a large discrepancy existed in the JJJ emissions among downscaled country-level emission inventories, with total emissions ranging from 657 to 1132 Mt CO2 (or 849 ± 214 for mean ± standard deviation (SD)) in 2012, while emission estimates based on provincial-level data estimated emissions to be 1038 and 1056 Mt. Compared to the mean emissions of city-data-based inventories (989 Mt), provincial-data-based inventories were 6% higher, and national-data-based inventories were 14% lower. Emissions from national-data-based inventories were 53–75% lower in the high-emitting industrial cities of Tangshan and Handan, while they were 47–160% higher in Beijing and Tianjin than those from city-data-based inventories. Spatially, the emissions pattern was consistent with the distribution of urban areas, and urban emissions in Beijing contributed 50–70% of the total emissions. Higher emissions from Beijing and Tianjin resulted in lower estimates of prefectural cities in Hebei for some national inventories. Conclusions National-level data-based emission inventories produce large differences in JJJ prefectural city-level emission estimates. The city-level statistics data-based inventories produced more consistent estimates. The consistent spatial distribution patterns recognized by these inventories (such as high emissions in southern Beijing, central Tianjin and Tangshan) potentially indicate areas with robust emission estimates. This result could be useful in the efficient deployment of monitoring instruments, and if proven by such measurements, it will increase our confidence in inventories and provide support for policy makers trying to reduce emissions in key regions.