In the context of China’s “double carbon” goal, pollution and carbon reduction is a consensus. As a demonstration area and model area for China’s development, how to take the lead in realizing the synergistic improvement of pollution and carbon reduction and embark on a green and low-carbon development path with Chinese characteristics is a common concern of the scientific community and the public. However, each city in Guangdong-Hong Kong-Macao Greater Bay Area (GBA) is different regarding resource endowment, energy structure, development conditions, and technical level. The efficiency, ability, and potential of pollution and carbon reduction must differ. The mission objectives, methods, and methods of promoting the “double carbon” work are also different. Only by considering it from the perspective of system collaboration can the “double carbon” work be safe and sustainable. The study proposes that we can, from the dynamic perspective of the production network and industrial transfer, integrate multi-source and multi-mode data and use a multi-scale evaluation method to analyze the multi-dimensional features and driving factors of the interaction effect of pollution and carbon reduction in GBA. The research results can help cities in GBA to understand their weak links in pollution and carbon reduction in a timely, comprehensive, and accurate manner. In addition, this study is conducive to providing decision-making reference for China to formulate regional synergistic effects.