Since the 21st century, the world has increasingly focused on the issue of sustainable development, and the green transformation issues have become a new hot topic worldwide. Green and low-carbon transformation has become an international consensus. Urban agglomerations are important connections between urban development and regional coordination, as well as important spatial carriers for economic activities. They are not only the main source of carbon emissions, but also the main battlefield for energy conservation and emission reduction. As an important field for carbon reduction, the green transformation of cities is crucial for achieving the “dual carbon” goals. This article focuses on 48 cities in the three most mature and influential urban agglomerations in China from 2011 to 2019, namely, the Beijing-Tianjin-Hebei urban agglomeration, the Yangtze River Delta urban agglomeration, and the Pearl River Delta urban agglomeration. The three-stage DEA model and Malmquist index model are used to measure the green transformation efficiency of the three urban agglomerations from both dynamic and static perspectives, and a Tobit regression model is constructed to explore the influencing factors of green transformation efficiency in urban agglomerations. Research has found that: 1) From a static perspective, the overall efficiency of green transformation in the three major urban agglomerations is at a high level, but from a temporal perspective, it shows a downward trend. The Pearl River Delta urban agglomeration is known for its green development, with the highest average efficiency of green transformation, followed by the Yangtze River Delta urban agglomeration. The Beijing-Tianjin-Hebei urban agglomeration has the lowest level of green transformation; 2) From a dynamic perspective, technological progress is the main driving factor for improving the efficiency of green transformation in the three major urban agglomerations. Therefore, the government should pay special attention to the progressiveness of technology when formulating relevant policies to promote urban green transformation; 3) From the perspective of spatiotemporal differences, there are significant differences in the spatiotemporal characteristics of green transformation among the three major urban agglomerations, and there are significant differences in green transformation strategies among different urban agglomerations. Eliminating environmental factors and random interference is necessary for accurately measuring the efficiency of green transformation in urban agglomerations; 4) From the perspective of influencing factors, factors such as industrial structure upgrading, green innovation level, and environmental regulation intensity jointly affect the efficiency of green transformation in urban agglomerations. Based on this, we should pay attention to the differences between urban agglomerations and implement policies tailored to local conditions; Strengthen the network system of urban agglomerations and avoid conflicts between cities; Encourage green technology innovation, accelerate industrial structure upgrading, and so on. This article focuses on the issue of green transformation in urban agglomerations, and conducts research from three perspectives: efficiency measurement, influencing factors, and implementation mechanisms. A relatively systematic theoretical framework for green transformation in urban agglomerations is formed, and an evaluation index system for green transformation efficiency in urban agglomerations is constructed and optimized. The composition mechanism of the five dimensional evaluation system for transformation efficiency is analyzed, and the bottleneck and breakthrough direction of the three major urban agglomerations in China in the development process are grasped. It has a good demonstration effect on the green transformation of other urban agglomerations.