With large-scale urbanization and dramatic economic development, the deterioration of urban ecological pollution and excessive consumption of resources in Chinese cities have turned into serious challenges. Due to the lack of resources and environment protection, natural assets are become increasingly scarce. In order to achieve sustainable urbanization, it is important to improve the well-being of urban residents within the restricted ecological resources. Ecological well-being performance (EWP) reflects the trends in well-being level and ecological consumption. In order to evaluate urban EWP, an index system is established in the perspective of input-output. After that, a case study of 30 provincial capital cities in China from 2011 to 2016 is presented, in which the Super-slack-based measure model (Super-SBM) is utilized. The results show that (1) the average EWP value of 30 provincial capital cities was low with the value of 0.89, but it has an overall improvement during 2011-2016; (2) the average EWP of Haikou was the highest, followed by Changsha and Beijing, while the bottom three EWP performers were Urumqi, Lanzhou and Xining; (3) spatially, capital cities in east and central regional provinces of China ranked first and second, while the capital cities in the northeast and west regions were ranked third and fourth according to the EWPs, respectively. In order to improve the EWP for 30 provincial capital cities, policy suggestions are proposed to make urban well-being improvement more ecologically efficient. The results from this study will provide valuable guidance to urban managers for designing and taking effective steps, allowing the Chinese cities to progress towards sustainable urban development.