Based on the energy–economy–environment–society (3E1S) system theory, this paper constructed a comprehensive evaluation system for the coordinated development of China’s ecological civilisation construction using panel data from 31 provinces and cities from 2005 to 2020, which is specifically divided into four sub-systems, namely, energy, economy, environment, and society, and covers 10 ordinal covariates and 40 ordinal variable indicators. In terms of measurement and evaluation methods, this paper adopted the composite system synergy model to measure the level of coordinated development of ecological civilisation construction of the country as a whole and 31 provinces and cities and adopted Arcgis maps, standard deviation ellipses, kernel density curves, and Theil index methods to explore the spatial-temporal evolution characteristics and regional differences in the level of coordinated development of ecological civilisation construction. It was found that the coordinated development level of China’s ecological civilisation construction increased year by year from 2005 to 2020, with the most obvious upward trend from 2011 to 2015, with an average increase of 26.5%. Secondly, the spatial distribution pattern of the coordinated development level of China’s ecological civilisation construction was relatively stable, basically showing a dominant southwest–northeast direction, but the spatial centre of gravity shows a trajectory shifting towards the southwest. Finally, there were large regional differences in the level of coordinated development of China’s ecological civilisation, with an overall decreasing regional pattern of “Central-Northeast-East-West”. However, the overall differences among the four regions showed a decreasing trend. The overall differences among the four regions were mainly intra-regional, with the western region having the greatest intra-regional differences and contributing to the overall differences. Although this paper takes China as a case study, its research methodology and conclusions can provide references for the construction of ecological civilisation and green sustainable development in other countries.