Urban agglomerations are the key areas to promote carbon dioxide (CO2) reduction. Understanding the association of CO2 emission of urban agglomerations and their influencing factors is significant to promote the synergistic management of carbon reduction in the Yangtze River Economic Belt (YREB). Based on the CO2 emission data of the three major urban agglomerations in the YREB from 2010 to 2020, this study summarised characteristics of the CO2 emission association structure of the three major urban agglomerations, explored the factors affecting the spatial association of CO2 emissions of in each urban agglomeration, and proposed countermeasures to promote the collaborative CO2 reduction of the urban agglomerations in the YREB accordingly. Results show that the CO2 emissions and correlations of the three urban agglomerations increase year by year, and the CO2 emission correlations have the spatial characteristics of “dense in the east and sparse in the west,” and the network correlation characteristics differ significantly among urban agglomerations. The CO2 emission linkage of the YREB has formed a block division with urban agglomerations as the boundary, and the linkages between urban agglomerations are relatively weak. The status and role of each city in the synergistic emission reduction network are different, and the formation paths and influencing factors of CO2 emission association are different among urban agglomerations; therefore, differentiated synergistic emission reduction policies need to be formulated for each region. The above findings provide realistic support for constructing a synergistic CO2 reduction strategy in a first-before-supporting and differentiated manner.