Urban agglomerations, such as Beijing-Tianjin-Hebei Region, Yangtze River Delta and Pearl River Delta, are the key regions for energy conservation, carbon emission reduction and low-carbon development in China. However, spatiotemporal patterns of CO2 emissions at fine scale in these major urban agglomerations are not well documented. In this study, a back propagation neural network based on genetic algorithm optimization (GABP) coupled with NPP/VIIRS nighttime light datasets was established to estimate the CO2 emissions of China’s three major urban agglomerations at 500 m resolution from 2014 to 2019. The results showed that spatial patterns of CO2 emissions presented three-core distribution in the Beijing-Tianjin-Hebei Region, multiple-core distribution in the Yangtze River Delta, and null-core distribution in the Pearl River Delta. Temporal patterns of CO2 emissions showed upward trends in 28.74–43.99% of the total areas while downward trends were shown in 13.47–15.43% of the total areas in three urban agglomerations. The total amount of CO2 emissions in urban areas was largest among urban circles, followed by first-level urban circles and second-level urban circles. The profiles of CO2 emissions along urbanization gradients featured high peaks and wide ranges in large cities, and low peaks and narrow ranges in small cities. Population density primarily impacted the spatial pattern of CO2 emissions among urban agglomerations, followed by terrain slope. These findings suggested that differences in urban agglomerations should be taken into consideration in formulating emission reduction policies.