As the development of Yangtze River Delta urban agglomeration has been upgraded to a national level development strategy in China, relevant regions need to pay more attention to the environmental governance issues. Based on the 2013–2018 development data of 41 cities and the established evaluation indicator system with “press-state-response” (PSR) model, we mainly use a combination of global principal component analysis (GPCA) and entropy method to comprehensively measure regional environmental governance performance (EGP) in the Yangtze River Delta urban agglomeration. Next, the spatial relationship is explored and discussed with spatial autocorrelation analysis. Finally, the panel Tobit model is used to perform a regression analysis on the factors affecting the performance of environmental governance in the Yangtze River Delta region. The results are summarized as follows. (1) From 2013 to 2018, the overall environmental governance performance of the Yangtze River Delta region maintained a steady growth trend, of which the environmental governance performance of Jiangsu Province and Shanghai maintained a steady increase, and the environmental governance performance of Anhui and Zhejiang Province fluctuated greatly. (2) These cities with better EGP are mainly located in the central and southern regions of the Yangtze River Delta, and those cities with poor EGP are mainly located in the northern part of the Yangtze River Delta. The environmental governance performance gap between provinces and cities is obviously large, and there are significant spatial positive correlations, spatial spillover effects and a trend of agglomeration with increased volatility. (3) The regression analysis shows that the economic development level has a significant positive impact on the EGP of the Yangtze River Delta region. Meanwhile, the negative impact of industrial structure and foreign investment is significant, but the positive impact of R&D investment intensity is insignificant, on the performance of environmental governance in the Yangtze River Delta region.