Urban agglomerations (UAs) are not only highly integrated economic communities but also communities of shared destiny with integrated environmental protection and ecological construction. Although low-carbon development within UAs has garnered significant attention, a lack of comprehensive analysis remains regarding the imbalances and driving factors influencing carbon emission efficiency (CEE) in these regions. This study investigates the CEE of China's five national UAs from 2006 to 2020 by incorporating the meta-frontier framework into the super slack-based model. The global Malmquist index analyzes dynamic trends in CEE by decomposing the total factor productivity of carbon emissions to examine the catch-up, innovation, and technological leadership effects. In addition, this paper employs the Theil index to explore the disequilibrium of CEE among the five UAs. Outcomes reveal that, first, CEE has regional heterogeneity, with the Pearl River Delta UA (PRDUA) having the highest CEE and the Beijing–Tianjin–Hebei UA (BTHUA) having the lowest CEE. The gap between BTHUA's CEE and that of other UAs is widening. Second, the overall CEE holds improvement room, with its disequilibrium resulting from uneven city growth within the UA. Third, the innovation effect is the key to improving CEE. Fourth, PRDUA serves as the technical leader among all UAs, while the two UAs in the inland area possess the potential for technical leadership. Finally, drawing from the empirical results, this paper provides specific suggestions for advancing industrial transformation, boosting innovation capabilities, and minimizing internal imbalances within UAs. The goal is to steer UAs in China toward low-carbon development.