The development of urbanization and the protection of the ecological environment are important aspects of sustainable development in city clusters, and their coordination and synergy are crucial to achieve this. Regarding the relationship between urbanization and the ecological environment, scholars both in China and internationally have conducted extensive research from the perspective of coordinated development. However, there is a lack of research on the synergistic effects of urbanization and the ecological environment. Taking the Chengdu-Chongqing city cluster as an example, this study uses the Haken model to analyze the synergistic evolution mechanism, development patterns, and future trends of urbanization and the ecological environment. This study draws the following conclusions: (1) while a synergistic development mechanism has been established between urbanization and the ecological environment, the current system is still in a stage of low-level synergy, and the control system’s parameter for the direction and path of evolution is urbanization. (2) From 2001 to 2020, the level of synergistic development between urbanization and the ecological environment was relatively low, mainly moving from low-level synergy to medium-low-level synergy to medium-level synergy. (3) There is a significant spatial disparity in the levels of synergistic development, for which the leading region centers on Chengdu and Chongqing in the northwest and southeast, respectively, and the lagging region comprises the eastern part of the city cluster, mainly represented by Dazhou, Kaizhou, and Yunyang. (4) The future trend of synergistic development between urbanization and the ecological environment in the Chengdu-Chongqing city cluster is promising but requires increased infrastructure construction in mountainous urban areas, enhanced cooperation and circulation in transportation, logistics, information and other aspects, and balanced improvements in the level of synergistic development between urbanization and the ecological environment. The study of the synergistic development effect of urbanization and the ecological environment in city clusters is of great significance for reducing the negative impact of urbanization on the ecological environment, increasing the positive interaction between the two, and promoting sustainable development in city clusters.