Ecological well-being performance (EWP) is central to achieving coordinated and sustainable economic and social development and environmental protection. This study constructed an evaluation index system of EWP, measured the EWP of 30 Chinese provinces or cities from 1997 to 2018 using the super-efficiency slack-based model (Super-SBM), and analyzed the spatial and temporal evolutionary characteristics of EWP. Under the division of four regions and eight regions, the Dagum Gini coefficient decomposition is applied to analyze the regional differences and sources of differences in EWP in China. Then, the Geographically and Temporally Weighted Regression (GTWR) model analyzes the factors influencing EWP. Results show that the inter-provincial differences in EWP in China are significant, with the eastern region having significantly higher EWP than the western, central, and northeastern regions. From 1997 to 2018, the overall spatial differences in EWP in China decreased. The four regions and eight regions show that reducing inter-regional differences is the key to mitigating regional unbalance in China. Urbanization significantly enhances EWP in China and the degree of openness and industrial structure has a significant heterogeneous effect on EWP. Therefore, future policy formulation should focus on transforming the economic development model, promoting coordinated regional development, and exploring the optimal ways to improve EWP according to local conditions. This study aims to provide a scientific basis and reference for promoting sustainable regional economic and social development and improving the imbalance.