The construction of ecological civilization is an important part of the cause of Chinese socialism, and the evaluation of the construction of ecological civilization and the differentiated analysis of its synergistic development will guide the coordinated development and coordinated ecological governance and protection in China. Synergistically, an evaluation index system was constructed based on the social–economic–natural multisystem, and the deviation coefficient coupling coordination model was used to evaluate the construction of the ecological civilization of 83 cities in the region from 2000 to 2020. The spatial and temporal development characteristics were explored using the spatial autocorrelation index and standard deviational ellipse, and the urban–rural differences were quantitatively analyzed by using the Thiel index. The results show that from 2000 to 2020, the degree of coordinated development of the social–economic–natural multisystem in different cities was low, and there are different reasons for cities with different urban–rural divisions. In this study region, the spatial distribution of the social–economic–natural coordinated development of cities is becoming increasingly discrete, and the center of urban distribution, which has a higher level of coordinated development, is gradually shifting to the southwest. In 2020, the level of coordinated social–economic–natural development in the study area was significantly different in urban and rural areas.