The Yangtze River Delta (YRD) urban agglomeration is an important engine of China's economic development. It is of great practical significance to explore the ecological welfare performance of the YRD for its high-quality development. From the perspective of resource allocation, under the transformed structure of ecological welfare performance consisting of ecology-economy-welfare, a two-stage chained super-efficiency DEA model considering the weak disposability of non-desired intermediate outputs was used to measure the global ecological welfare performance of the YRD urban agglomeration and the efficiency at different stages in 2011-2021. A spatial Durbin model with double-fixed effects was utilized to reveal the ecological welfare performance of the YRD urban agglomeration. The spatial spillover effect was also utilized to explore the improvement path of ecological welfare performance of the YRD urban agglomeration. The results show that: (1) The overall eco-welfare performance of the YRD urban agglomeration maintained a stable average level of around 0.8, but it was noteworthy that as high as 68.3% of the cities have not reached an effective state. At the same time, the significant differences in eco-welfare performance among cities reflected the uneven utilization efficiency of resources and also revealed the challenges and disparities in environmental protection and sustainable development efforts across different cities. (2) The internal composition of the YRD urban agglomeration exhibited disparities, with an ecological social-economic efficiency of 0.685 and an economic-welfare efficiency of 0.863. These disparities mainly came from imbalances within the three provinces and one city, contributing to rates of 77.39% and 77.14%, respectively. This unbalanced development presents challenges in terms of environmental protection, socio-economic integration, and welfare distribution. Therefore, targeted measures are imperative to foster balanced and sustainable development across the region. (3) Spatially, the ecological-welfare performance of the YRD urban agglomeration has strongly positive spatial correlation, while the greening coverage of built-up areas, the rate of harmless treatment of domestic waste, GDP per capita, urban per capita annual consumption, and government intervention have positive promotion effects on the regional integration of the YRD urban agglomeration, and the greening coverage of built-up areas and the rate of harmless treatment of domestic waste have certain spatial spillover effects. (4) The three categories of low economy-high welfare (L-H), low economy-low welfare (L-L), and high economy-high welfare (H-H) have the largest number of cities and are more evenly distributed. The number of cities belonging to the high economy-low welfare (H-L) category is the smallest. In terms of upgrading paths, unilateral breakthroughs are the best way for most cities to compensate for their inefficiency.