In order to participate in global competition and international cooperation, urban agglomeration serves as the main geographical unit to promote China's new urbanization in recent years. This study investigated the driving mechanism of carbon emissions during the rapid urbanization over the past 15 years (2000-2014) in China. We selected six representative cities in typical urban agglomerations including Beijing, Tianjin, Shanghai, Guangzhou, Wuhan, and Chongqing. The factor decomposition method was used to quantify the spatial patterns and drivers of carbon emissions. Four factors were used to analyze the driving mechanism for carbon emissions, including the population scale effect, economic development effect, energy intensity effect, and energy structure effect. Another four factors were calculated to quantify the urbanization characteristics in these cities, including the carbon emission intensity, energy intensity of economic activity, per capita GDP, and year-end total population. The results showed that the total economic levels in all urban agglomerations are growing and the energy efficiency is improved stably. These urban agglomerations have different proportions of energy sources and significant changes in carbon emissions. The intensity of carbon emissions declined in the cities of Beijing, Shanghai, and Chongqing whereas it increased in Tianjin. Comparably, the intensity of carbon emissions was stable in Guangzhou and Wuhan. Secondly, the results showed that the income effect and population effect in urban agglomerations have positive effects on the driving mechanism of carbon emissions whereas energy intensity has negative effects. We also note that the carbon intensity of carbon emissions remains uncertain. Generally, the effects of four driving factors on carbon emissions increased gradually from 2000 to 2014 in Tianjin and Guangzhou. These effects were stable in Beijing and Shanghai during this period. Interestingly, the cities of Wuhan and Chongqing have a curve trend with a decrease at first and then an increase. This study focused on the driving factors of carbon emissions in typical urban agglomerations of China. The results help to support policy-making on carbon-emissions trading in urban agglomerations and provide practical strategies for urban agglomeration management.