Attaining optimal eco-efficiency is of paramount importance in promoting the sustainable and harmonious development of the economy and environment within urban agglomerations. Firstly, this paper utilizes the Super-SBM model with undesirable output to measure the eco-efficiency (EE) of 64 cities in the Beijing–Tianjin–Hebei metropolitan region (BTHMR), the Yangtze River Delta (YRD), the Pearl River Delta (PRD), and the Chengdu–Chongqing Economic Zone (CCEZ) from 2006 to 2019. Secondly, this study puts forth a novel and comprehensive index system aimed at evaluating the urbanization efficiency and sheds light on the spatiotemporal changes in EE and urbanization efficiency. Finally, the STIRPAT model is used to examine the influencing factors of EE and to investigate the correlation between EE and urbanization efficiency. The study found that the overall EE of the four typical urban agglomerations is high, but the trend varies with a decrease of about 12.9% from 2006 to 2019. The mean EE is in the order of CCEZ > PRD > BTHMR > YRD, with mean values of 0.941, 0.909, 0.842, and 0.732, respectively. The level of science and technology and the urbanization efficiency have a significant positive impact on EE, while population, industrial structure, FDI, and greening level have an inhibitory effect on urban eco-efficiency. Based on the results, policy suggestions such as paying attention to regional heterogeneity and giving full play to the government’s macro-regulatory role in shaping the economic and industrial structure are proposed to serve as a guide for the coordinated development of urban agglomerations under the Dual Carbon Target.