After rapid development in recent decades, China has laid a strong economic foundation and established material conditions. Despite this, the country still confronts a range of challenges that impede higher-quality economic and social development. To measure high-quality regional development, eco-wellbeing performance (EWP) has become an important tool that seeks to strike a balance between economic development, human wellbeing, and environmental protection. This paper proposes a three-stage network efficiency evaluation model to decompose EWP into three stages, namely ecological economic efficiency (EEE), economic innovation efficiency (EIE), and innovation wellbeing efficiency (IWE). A directional distance function (DDF) model was utilized to assess the overall EWP efficiency and phase-in efficiency for 248 cities over the period from 2016 to 2020. The study results indicate that EWP in China is generally low. In terms of the three sub-stages of EWP, the first stage performs optimally, the third stage performs the second best, and the second stage is the worst. The research suggests that the principal reason for the generally low EWP may be linked to the efficiency of the transformation of economic investments into innovative outcomes in the second stage. From a regional viewpoint, EWP generally shows a gradually decreasing trend from the east, central, and west to the northeast, but the stage performance varies among regions. The eastern region has lower EEE, but both EIE and IWE perform better than the national average; the central region is well-balanced between the three stages; the western region leads the country in EEE, but lags in both EIE and IWE; and the northeast region has inferior performance in all stages. This study’s findings provide vital reference values for policy-makers to determine key points for enhancing EWP in different regions of China.