With rapid urbanization and industrialization, ecological disorders and environmental degradation have become serious, and the promotion of the coordinated development of the social economy and ecological environment is not only a pressing problem to be solved, but also an important step towards sustainable development. The coordinated development of the social economy and eco-environment is conducive to sustainable development. Considering the Chengdu–Chongqing urban agglomeration as a case study, this paper adopts panel data and establishes an index system to evaluate the coupling coordination degree (CCD) between the social economy and ecological environment based on the concept of high-quality development. From the perspective of time and space, the changing laws and characteristics of the CCD are analyzed, and the key factors affecting it are determined using regression analysis. The results show the following: (1) the CCD between the social economy and ecological environment of the Chengdu–Chongqing urban agglomeration presents a low level overall; (2) the CCD in more developed regions is significantly higher than that in less developed regions; thus, the characteristics of spatial differences are obvious; (3) the urbanization rate, ratio of actual use of foreign capital and GDP, ratio of total export-import volume and GDP, proportion of days with good air quality, and per capita public green space area are the main factors affecting the coordinated development of the social economy and ecological environment in the Chengdu–Chongqing urban agglomeration; and (4) Chongqing has obvious endogeneity. Finally, corresponding policy recommendations are provided aimed at promoting rapid economic development in the Chengdu–Chongqing urban agglomeration while focusing on environmental protection and promoting high-quality economic development with ecological environmental protection, while putting forward decision-making suggestions for high-quality development of urban agglomerations.