The sustainable development of ecologically fragile areas and the implementation of regional coordinated development strategies cannot be separated from the coordinated development and common progress of urbanization and the ecological environment, and this is particularly the case in Southwest China. This study examines the interplay between urbanization and the ecological environment across 26 cities in Southwest China from 2009 to 2019, utilizing 30 statistical indicators to analyze their coupling coordination relationship and its spatiotemporal evolution. The Entropy TOPSIS method, the coupling coordination degree model, and the obstacle factors model were used to calculate the subsystem score, coupling coordination degree, and obstacle factors, respectively. Our findings reveal an upward trajectory in urbanization scores across the 26 cities, juxtaposed with a fluctuating downward trend in ecological environment scores. The coupling coordination degree of urbanization and ecological environment in most cities maintained a rapid upward trend and showed spatial distribution characteristics of “strong core, weak middle, and edge.” Moreover, our analysis identified public transport facilities, aggregate purchasing power, and cultural supply service services as primary obstacle factors impeding the development of coupling coordination degrees. These research results offer valuable insights for informing future endeavors in achieving high-quality development and fostering ecological civilization.