In this study, based on ecosystem service theory, the contribution rate of ecosystems was introduced to improve the ecological well-being accounting method. On this basis, the spatial and temporal characteristics of per capita ecological well-being and ecological-economic efficiency were analyzed. In order to further clarify the policy implication of the evaluation results, a classification model of ecological well-being based on the perspective of relative equity and efficiency was proposed, ecological well-being was classified by relative well-being index and relative efficiency index, and the spatial and temporal distribution patterns of different types of ecological well-being was analyzed from 2000 to 2015 for 337 cities at prefecture-level and above in China. The research results can provide some references for promoting the construction of ecological civilization in China. The results indicate that during the study period the spatial distribution of per capita ecological well-being and ecological-economic efficiency of the 337 cities was very different in the two regions northwest and southeast of the “HU line,” their centers were located in Yushu Prefecture of Qinghai Province and Xinyang City of Henan Province, respectively, and moved to the northeast and southwest directions. A negative spatial correlation between ecological-economic efficiency and per capita ecological well-being was identified by the bivariate spatial autocorrelation method. The high-low clusters were mainly located in the eastern coastal cities of Hebei, Shandong, Jiangsu, Shanghai, and some cities of Anhui and Henan; the low-high groups were mainly gathered in the western cities; the low-low clusters were mainly located in Shanxi, Henan, and Anhui Provinces. The relative well-being and relative efficiency indices were used to classify the study area into four categories: the high efficiency-low well-being zone was mainly distributed in Hebei, Shandong, Shanxi, Henan, and Jiangsu Provinces; the low efficiency-high well-being zone was mainly distributed in western cities, most cities in the northeast, and cities in the southeast; the low efficiency-low well-being zone was mainly located at the junction of high efficiency-low well-being zone and low efficiency-high well-being zone; the high efficiency-high well-being zone was scattered. To realize the construction of ecological civilization in all regions of China, it is necessary to enhance the ecological-economic efficiency in the western region and the per capita ecological well-being in the eastern region.