As a critical engine for national economic growth, mega urban agglomerations have significant scale effects and economic and environmental spillover effects. This paper aims to study the green and low-carbon coordinated development of mega urban agglomerations to evaluate the country’s level of ecological civilization and its green and low-carbon development. The traditional research on green and low-carbon urban development tends to homogenize the redistribution theme, leading to significant errors in spatial allocation. This results in a lower accuracy of spatial distribution calculations for green development. Additionally, the research is constrained by data precision and methodology, making it challenging to measure the spatial differences in green and low-carbon development within urban clusters at the block level. This limitation hinders the ability to conduct detailed studies on the efficiency variations of green and low-carbon development in urban clusters. To achieve this aim, the study adopts the DPSR framework of the economic, resource, social, and ecological environment complex system and focuses on the Guangdong-Hong Kong-Macao Greater Bay Area in China. The study uses the entropy method, Gini coefficient method, and non-expected output super-efficiency SBM model to analyze the spatial effects and development efficiency of green and low-carbon development in this region from 2006 to 2020. The study results indicate that: (1) the overall level of green and low-carbon development in the Greater Bay Area is on the rise, with Shenzhen, Guangzhou, Foshan, and Zhuhai showing more stable development than other cities. Foreign direct investment and fixed asset investment in science and technology have significantly promoted green and low-carbon development. (2) The spatial differences in the region’s level of green and low-carbon development have narrowed trends, mainly due to differences between regions. However, well-developed cities such as Guangzhou and Shenzhen have taken the initiative to lead the development of other cities, fully leveraging their advantages in science and technology, geographical location, and other resources to promote the improvement of the external orientation of other cities. (3) The overall development efficiency of green and low-carbon in the Greater Bay Area is on the rise, with Guangzhou region showing overall stability, and Shenzhen region and Zhuhai region experiencing multiple ups and downs in their development. The three sub-regions show significant differences, but the balance and coordination of development have significantly improved. Finally, this study provides theoretical support for the future green and low-carbon development of urban clusters. It is advantageous for integrating the mainstream policy analysis framework of environmental economics with the complex adaptive systems of urban clusters. The research expands the boundaries of existing theoretical studies and offers new methodological approaches for interdisciplinary research. The study achieves a balance between the opportunity effects of green and low-carbon development and environmental policy constraints in super large urban clusters, effectively enhancing resource utilization efficiency in these clusters.