An emergy analysis is used to assess the sustainability of urban agglomerations’ eco-economic systems, which are generally measured by emergy–value sustainability indicators using a combination of several system indicators. However, this assessment approach is not applicable to economically developed high-density urban agglomerations. The application of the traditional entropy value evaluation method needs to be expanded to further strengthen the sustainability of the complex eco-economic–social relationships in megacity cluster regions. In this study, taking the Guangdong–Hong Kong–Macau Greater Bay Area (GBA) as a case study, we study a new evaluation method for evaluating the sustainable development capacity of cities. This method is based on the entropy power method and is used to construct the evaluation system of all indicators of the social–economic–natural subsystems of the eco-economic system, and it couples the development degree with the coordination degree. (1) This study shows that the new method is applicable for the sustainability assessment of high-density megacity clusters and is more accurate and comprehensive. The sustainability rankings are provided for Zhaoqing, Jiangmen, Huizhou, Guangzhou, Macau, Foshan, Zhongshan, Dongguan, Zhuhai, and Shenzhen. Hong Kong is the most representative, with a high sustainability index, but has the lowest level of coordination and a clear incoherence within the system. (2) The current emergy structure of the GBA city cluster is extremely unreasonable. The GBA city cluster is a resource-consuming city with a common characteristic of a low level of coordinated development. Although urban clusters have some potential in terms of renewable emergy and resources, the recycling rate of waste is low, and the consumption rate of nonrenewable resources is high. The effective use of land resources has become an important factor in the bottlenecking of sustainable development, and all other cities face such problems, except Zhaoqing, Jiangmen, and Huizhou. (3) The GBA city cluster can be divided into three categories according to the new method. Category 1 mainly includes Hong Kong, Shenzhen, Dongguan, and Zhuhai, which have coordinated development degrees ranging between 0.0 and 0.135 and the highest emergy density (ED) values but are extremely dependent on external emergy. They have high levels of emergy use per capita (EUC), high living standards, and high quality of life. The effective use of land resources severely restricts sustainable economic development, resulting in extreme ecological and environmental carrying pressure. Category 2 includes Guangzhou, Macau, Foshan, and Zhongshan, whose coordinated development degrees range from 0.143 to 0.179. The sustainable development capacity of these cities is at the middle level amongst the whole GBA. Their main emergy characteristics are emergy flow and subsystem evaluation indices that are between category 1 and category 3, but each has its own characteristics. The category 3 cities include Zhaoqing, Jiangmen, and Huizhou, whose coordinated development degrees are between 0.192 and 0.369. These cities are characterized by relatively low ED and EUC values, living standards, and quality, but their land resources have certain potential. These cities have a high emergy self-sufficiency rate (ESR) and natural environmental support capacity, but their environmental loading ratio (ELR) is still much higher than the national average. In terms of the economic development and innovation development levels, these cities are ranked as category 1 > category 2 > category 3. In terms of the ecological and environmental conditions and blue–green space protection, these cities are ranked as category 1 < category 2 < category 3. The results of this study can provide cities in the GBA with more scientific and consistent directions for the coordinated development of their ecological–economic–social systems to provide sustainable development decision-making services for megacity cluster systems.