<p>The concepts of “natural capital” and “sustainable urban development” are garnering widespread attention as the role of the environment and ecology in promoting economic development and maintaining human well-being is increasingly acknowledged. However, prevailing approaches to accounting for natural capital in sustainable cities exhibit deficiencies, with many overlooking the value associated with the natural environment, ecology, and capital stock of these cities. To rectify this issue, we propose a framework for natural capital analysis and decision-making for sustainable cities (Environment-Ecology-Economy Sustainable Development, <i>EEE-SEEA</i>). This framework integrates environmental, ecological, and economic perspectives, employing <i>ArcGIS</i> software for the visualization and analysis of sustainable cities in China. The results indicate an inverted U-shaped development trend distribution for natural capital, with ecosystem service accounting displaying a stable trend. The estimation results for urban sustainable development show a consistent annual increase with a certain level of resource dependence. On a level, natural capital accounting reached its zenith in 2010, gradually declining in 2015 and 2021, thus validating the inverted U-shaped development trend distribution. Ecosystem service accounting has demonstrated continuous development over the years, with the “Hu Huanyong line” becoming a crucial reference for distribution. The degree of sustainable development among cities is on the rise, with the central and northern regions of China exhibiting higher overall development quality. By integrating natural capital accounting and ecosystem service assessment, it becomes evident that cities in eastern and southern China still have significant room for improvement in terms of their sustainable development trajectory.</p>