Ecological welfare performance contributes directly to human well-being and regional sustainable development. Improving the regional ecological welfare performance in the process of pursuing green and sustainable development demands theoretical innovation and empirical exploration. Based on the super-efficiency SBM model, this study evaluated the ecological welfare performance of 108 cities during the period of 2009 to 2019. The Dagum Gini coefficient decomposition and spatial convergence model were employed to analyze the differences in ecological welfare performance across and within the study area and explore the underlining causes of such spatial differentiation in the Yangtze River Economic Belt and the upper, middle and lower reaches. It can be seen from the results that: (1) the overall difference in the ecological welfare performance of the Yangtze River Economic Belt is associated with a fluctuating downward trend during the study period. Regional and inter-regional differences were revealed and hypervariable density was identified as the main source of the differences. (2) The ecological welfare performance of the Yangtze River Economic Belt has absolute and conditional β convergence, and the ecological welfare performance of each city-region and surrounding urban areas has a positive impact on each other. (3) The difference in the spatial-temporal differentiation trend is manifested by the difference in the convergence rate. The cities in the middle reaches of the Yangtze River have the fastest convergence rate, followed by the cities in the upper reaches, and the cities in the lower reaches are the slowest. This geographic difference is mainly driven by the combined effects of industrial structure, urban characteristics, environmental regulation, foreign direct investment, and transportation accessibility. Finally, it is proposed that future policies should focus on the imbalanced regional development in the study area, and each region needs to explore ways to improve local ecological welfare performance according to local conditions, and ultimately promote the overall green, coordinated and high-quality development in the Yangtze River Economic Belt.